From fmachadoj at inf.ufrgs.br  Sun Feb 15 08:19:29 2004
From: fmachadoj at inf.ufrgs.br (Fernando Machado)
Date: Sun, 15 Feb 2004 10:19:29 -0300
Subject: [EMBOSS] auth using jemboss
Message-ID: <402F71E1.60706@inf.ufrgs.br>

I?m having trouble using jemboss. evrth was fine, but authentication 
stopped working. Now I cant authenticate anymore.
do somebody knows what can i do?

thanks

Fernando Machado
UFRGS - II - 43424



From MAILER-DAEMON at tank.uams.edu  Wed Feb  4 10:13:52 2004
From: MAILER-DAEMON at tank.uams.edu (MAILER-DAEMON at tank.uams.edu)
Date: Wed, 04 Feb 2004 09:13:52 -0600
Subject: [EMBOSS] Undeliverable mail: 
Message-ID: <receipt-77613715@tank.uams.edu>

Failed to deliver to '<childsgwenv at exchange.uams.edu>'
RAV AntiVirus plugin for CommuniGate Pro has found a virus in the e-mail you are about to send. Your message is not delivered.

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From dsullivan at gradipore.com  Wed Feb  4 13:42:17 2004
From: dsullivan at gradipore.com (Dan Sullivan)
Date: Thu, 5 Feb 2004 05:42:17 +1100 
Subject: [EMBOSS] 18 Month Shelf Life and Free Buffer
Message-ID: <017AE08058A1D3118A7B0008C70D6217030116FA@GSYD_NT5>

 
 
   _____  

  <http://www.it3host.com/grad/GradiporeWebCast_files/headder.gif> 

 


  <http://www.it3host.com/grad/GradiporeWebCast_files/broch.gif> 

  <http://www.it3host.com/grad/GradiporeWebCast_files/line.gif> 	





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Gradipore LongLife gels represent the
next generation in precast gel innovation.
The LongLife gels use a Tris-HEPES-SDS
buffer system, that gives faster running
times, quicker transfer times and a longer
shelf life. The gels fit into most popular gel
running units.

Specifications:
To view the LongLife gel migration table click
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RefMenuID=84&Category=> here

To view recommended running conditions 
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Category=Life+Science+Separations> here

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Call: 877-592-1060. Place an order for a box of Gradipore LongLife gels and
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This e-mail and any files transmitted with it are confidential and intended
only for the use of the individual or entity to which they are addressed.
If you are not the intended recipient of this e-mail, you must not
disseminate, copy or otherwise use this information. If you have received
this e-mail in error, please notify Gradipore immediately. Thank you.


      
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From postmaster at eva.mpg.de  Wed Feb  4 18:38:45 2004
From: postmaster at eva.mpg.de (postmaster at eva.mpg.de)
Date: Thu,  5 Feb 2004 00:38:45 +0100 (CET)
Subject: [EMBOSS] VIRUS IN YOUR MAIL
Message-ID: <20040204233845.2421A206B8@email.eva.mpg.de>

                           V I R U S  A L E R T

Our viruschecker found the

	W32/Mydoom.a at MM

virus(es) in your email to the following recipient(s):

-> stoneking at eva.mpg.de

Please check your system for viruses, or ask your system administrator
to do so.
#
For your reference, here are the headers from your email:

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Received: from embnet.org (unknown [148.228.146.204])
	by email.eva.mpg.de (MPI EVAN Mailserver) with ESMTP id 773F820518
	for <stoneking at eva.mpg.de>; Thu,  5 Feb 2004 00:38:42 +0100 (CET)
From: emboss at embnet.org
To: stoneking at eva.mpg.de
Subject: Error
Date: Wed, 4 Feb 2004 17:44:04 -0600
MIME-Version: 1.0
Content-Type: multipart/mixed;
	boundary="----=_NextPart_000_0004_DC5C203D.89529525"
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From newsletter at prographicssportswear.com  Thu Feb  5 12:36:34 2004
From: newsletter at prographicssportswear.com (newsletter at prographicssportswear.com)
Date: Thu, 5 Feb 2004 12:36:34 -0500
Subject: [EMBOSS] Please send this email to your T-shirt ordering committee
Message-ID: <200402051736.i15HaYh08277@www.prographicssportswear.com>

You must use an HTML compliant e-mail client to view this message properly.

Visit http://www.prographicssportswear.com for more information.
-------------
Click the link to unsubscribe:
http://news.prographicssportswear.com/submit.php?id=27&le_email=emboss at embnet.org
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From aengus.stewart at cancer.org.uk  Thu Feb  5 13:44:06 2004
From: aengus.stewart at cancer.org.uk (Aengus Stewart)
Date: Thu, 05 Feb 2004 18:44:06 +0000
Subject: [EMBOSS] dbifasta possible problem
In-Reply-To: <20040130153412.E6096@uracil.uio.no>
References: <20040130153412.E6096@uracil.uio.no>
Message-ID: <40228EF6.5080108@cancer.org.uk>


I have been using Warren Gish's nrdb2 to create a non-redundant protein dataset

It generates FASTA title lines like

>swiss:ACDD_METMA Q8PRQ5 Acetyl-CoA decarbonylase/synthase complex delta subunit (ACDS complex delta subunit) (Corrinoid/iron-sulfur component small subunit).
trembl:Q8PRQ5 Q8PRQ5 CO dehydrogenase/acetyl-COA synthase delta subunit (EC 1.2.99.2).
refseqp:NP_632712 NP_632712 Methanosarcina mazei Goe1 CO dehydrogenase/acetyl-COA synthase delta subunit [Methanosarcina mazei Goe1]. 0/0
refseqp:NP_634109 NP_634109 Methanosarcina mazei Goe1 CO dehydrogenase/acetyl-COA synthase delta subunit [Methanosarcina mazei Goe1]. 0/0

Where it cats together the titles from the different DBs that have identical entries.

I have discovered that dbifasta will only accept -idformat simple to process this file

I assumed I could use -idformat gcgidacc

but this and any other -idformat bar simple causes dbifasta to "finish"

I say finish as there is no errors or complaints it just ends...........

I didnt expect this, is this correct behaviour?


Cheers
Aengus


-- 
----------------------------------------------------------------------------
Aengus Stewart
Group Leader
Computational Genome Analysis Laboratory  Tel: +44 (0)20 7269 3679
Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
----------------------------------------------------------------------------


From postmaster at wisair.com  Thu Feb  5 15:17:25 2004
From: postmaster at wisair.com (postmaster at wisair.com)
Date: Thu, 5 Feb 2004 22:17:25 +0200
Subject: [EMBOSS] Delivery Status Notification (Failure)
Message-ID: <0qd0HWTUX000009b5@wis.wisair.com>

This is an automatically generated Delivery Status Notification.

Delivery to the following recipients failed.

       dave at wisair.com



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From flavio.licciulli at ba.itb.cnr.it  Fri Feb  6 06:15:08 2004
From: flavio.licciulli at ba.itb.cnr.it (Vito Flavio Licciulli)
Date: Fri, 06 Feb 2004 12:15:08 +0100
Subject: [EMBOSS] dbiflat problem on TRU64
Message-ID: <5.1.0.14.0.20040206120037.045c7d80@area.ba.cnr.it>

I have a problem with dat database entries indexing with dbiflat. Sometimes 
the found entries are different from searched entries .

When I run for example:
$>seqret embl:u18650
Reads and writes (returns) sequences
Output sequence [rg9401257.fasta]:
$>more rg9401257.fasta
RG9401257 AJ401257.1 Rotavirus G9 partial VP7 gene for outer capside glycoprote
in, strain G9P[8], isolate 414/98
attatggaattaaatttaccgatcactggctccatggatacagcatatgcaaattcatca....

The search entry (u18650) comes from ROD division while the entry found 
comes from VRL division.
This is the embl definition in emboss.defaults:
DB embl [ type: N method: emblcd
                format: embl dir: $emboss_db_embl indexdir: 
$emboss_db_embl/INDEX
                exclude: *.dat  file: *.dat  comment: "EMBL sequences"]

I found the same problem in SWISSPROT too.

We have a Compaq TRU64Unix 5.1a, is something related to the dbiflat for 
this OS (sort problem,....) ? or what else?

Regards
         Flavio Licciulli

Vito Flavio Licciulli                          e-mail: 
flavio.licciulli at ba.itb.cnr.it
System & Database Administrator
Italian EMBnet Node
C.N.R. - ITB Sez.di BARI                Phone (39) 080-5482100/30
Via Amendola 168/5  BARI ITALY    Fax   (39) 080-5482607
----------------------------------------------------------------------------




From MAILER-DAEMON at pimail.pi-india.net  Mon Feb  9 05:37:20 2004
From: MAILER-DAEMON at pimail.pi-india.net (MAILER-DAEMON at pimail.pi-india.net)
Date: 9 Feb 2004 10:37:20 -0000
Subject: [EMBOSS] failure notice
Message-ID: <20040209100535.4E8727DDD9@mercury.hgmp.mrc.ac.uk>

Hi. This is the qmail-send program at pimail.pi-india.net.
I'm afraid I wasn't able to deliver your message to the following addresses.
This is a permanent error; I've given up. Sorry it didn't work out.

<brenda at yahoo.co.uk>:
195.50.106.7 does not like recipient.
Remote host said: 553 VS10-RT Possible forgery or deactivated due to abuse (#5.1.1)
Giving up on 195.50.106.7.

--- Below this line is a copy of the message.

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From: emboss at embnet.org
To: brenda at yahoo.co.uk
Subject: HELLO
Date: Mon, 9 Feb 2004 15:37:28 +0530
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------=_NextPart_000_0006_B1AA88D5.B26A025E--




From emeasmex at Roche.COM  Mon Feb  9 05:07:22 2004
From: emeasmex at Roche.COM (emeasmex at Roche.COM)
Date: Mon, 09 Feb 2004 11:07:22 +0100
Subject: [EMBOSS] [MailServer Notification]To Recipient virus found and action taken.
Message-ID: <0b0f01c3eef4$82712570$5c2af591@emea.roche.com>

ScanMail for Microsoft Exchange has detected virus-infected attachment(s).

Sender = owner-emboss at hgmp.mrc.ac.uk
Recipient(s) = emboss at embnet.org
Subject = [EMBOSS] failure notice
Scanning time = 2/9/2004 11:07:22 AM
Engine/Pattern = 6.810-1005/757

Action on virus found:
The message body contains PE_ELKERN.D virus. ScanMail has deleted the message body.

Warning to recipient. ScanMail has detected a virus.


From ".BE.ADM.BE2307.SHG_GATEWAY" at schering.de  Mon Feb  9 05:06:43 2004
From: ".BE.ADM.BE2307.SHG_GATEWAY" at schering.de (".BE.ADM.BE2307.SHG_GATEWAY" at schering.de)
Date: Mon, 9 Feb 2004 11:06:43 +0100
Subject: Virus Alert - ScanMail for Lotus Notes --> [EMBOSS] failure notice
Message-ID: <OFF13B927A.EDB56FA2-ONC1256E35.00378C01@eu.schering.net>

The virus protection system has detected and removed a virus in your email.


Date: 02/09/2004 11:06:43 AM
121:  [EMBOSS] failure notice
Virus:      PE_ELKERN.D
File: document.zip
From: owner-emboss at hgmp.mrc.ac.uk
To:   emboss at embnet.org
Action:     Uncleanable, Quarantined;

Scanned by ScanMail for Lotus Notes 2.51
with scanengine 6.510-1002
and patternfile lpt$vpn.757




From emboss at embnet.org  Tue Feb 10 01:33:32 2004
From: emboss at embnet.org (emboss at embnet.org)
Date: Tue, 10 Feb 2004 12:03:32 +0530
Subject: [EMBOSS] Returned due to virus; was: hello
Message-ID: <200402100634.i1A6YEXE245854@fserv1.yokohama-cu.ac.jp>



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From stefanielager at fastmail.ca  Fri Feb 13 02:54:53 2004
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Fri, 13 Feb 2004 07:54:53 +0000 (UTC)
Subject: [EMBOSS] Database access external app
Message-ID: <20040213075454.D402D86194C@mail.interchange.ca>

Hi,

I'm trying to retrieve entries in EMBOSS using fastacmd as an external
application. It works nice as long as the database, indexed with
formatdb, is a singe fasta file. But when I have big databases that are
split up in volumes and use a .nal file with the names of the idividual
files it doesn't work with EMBOSS anymore. Does anyone have experience
with fastacmd and EMBOSS database indexing in combination with databases
split into volumes?

Stefanie 
_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians


From Marc.Logghe at devgen.com  Fri Feb 13 03:15:59 2004
From: Marc.Logghe at devgen.com (Marc Logghe)
Date: Fri, 13 Feb 2004 09:15:59 +0100
Subject: [EMBOSS] Database access external app
Message-ID: <BEE28BF86078B6429D6C780635718E21904B88@morelia.be.devgen.com>

Hi Stefanie,
Can you show the actual entry in your emboss.default file, or eventual error messages when running the emboss command ?
We use exactly the same system for the worm chromosomal sequences for instance. Every chromosome is a separate blastable 'database'. worm_chromosomes.nal makes them look like 1 big.
The entry looks like this:
DB worm_chromosomes [
   type: N
   format: ncbi
   method: app
   app: "fastacmd -d worm_chromosomes -s %s"
]

HTH,
Marc

> -----Original Message-----
> From: Stefanie Lager [mailto:stefanielager at fastmail.ca]
> Sent: vrijdag 13 februari 2004 8:55
> To: emboss at embnet.org
> Subject: [EMBOSS] Database access external app
> 
> 
> Hi,
> 
> I'm trying to retrieve entries in EMBOSS using fastacmd as an external
> application. It works nice as long as the database, indexed with
> formatdb, is a singe fasta file. But when I have big 
> databases that are
> split up in volumes and use a .nal file with the names of the 
> idividual
> files it doesn't work with EMBOSS anymore. Does anyone have experience
> with fastacmd and EMBOSS database indexing in combination 
> with databases
> split into volumes?
> 
> Stefanie 
> _________________________________________________________________
>     http://fastmail.ca/ - Fast Secure Web Email for Canadians
> 


From stefanielager at fastmail.ca  Fri Feb 13 03:53:19 2004
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Fri, 13 Feb 2004 08:53:19 +0000 (UTC)
Subject: [EMBOSS] Database access external app
In-Reply-To: <BEE28BF86078B6429D6C780635718E21904B88@morelia.be.devgen.com>
Message-ID: <20040213085320.4F6E7863CFF@mail.interchange.ca>

Marc,

I use the same setup as you "app: "fastacmd -d hs_pub_genomic -s %s",
and I try to retrive from a human genome database (each chr is a BIG
fasta file). The formatdb indexing seems OK, fastacmd works on
commandline. But I don't get any error from EMBOSS it just can't retrive
entries (it just hangs there forever). 

Stefanie

> Hi Stefanie,
> Can you show the actual entry in your emboss.default file, or eventual
> error messages when running the emboss command ? We use exactly the
> same system for the worm chromosomal sequences for instance. Every
> chromosome is a separate blastable 'database'. worm_chromosomes.nal
> makes them look like 1 big. The entry looks like this: DB
> worm_chromosomes [ type: N format: ncbi
> method: app
> app: "fastacmd -d worm_chromosomes -s %s"
> ]
> 
> HTH,
> Marc
> 
>> -----Original Message-----
>> From: Stefanie Lager [mailto:stefanielager at fastmail.ca]
>> Sent: vrijdag 13 februari 2004 8:55
>> To: emboss at embnet.org
>> Subject: [EMBOSS] Database access external app
>> 
>> 
>> Hi,
>> 
>> I'm trying to retrieve entries in EMBOSS using fastacmd as an
>> external application. It works nice as long as the database, indexed
>> with formatdb, is a singe fasta file. But when I have big
>> databases that are
>> split up in volumes and use a .nal file with the names of the
>> idividual
>> files it doesn't work with EMBOSS anymore. Does anyone have
>> experience with fastacmd and EMBOSS database indexing in combination
>> with databases
>> split into volumes?
>> 
>> Stefanie
>> _________________________________________________________________
>> http://fastmail.ca/ - Fast Secure Web Email for Canadians
>> 
_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians


From Marc.Logghe at devgen.com  Fri Feb 13 04:43:55 2004
From: Marc.Logghe at devgen.com (Marc Logghe)
Date: Fri, 13 Feb 2004 10:43:55 +0100
Subject: [EMBOSS] Database access external app
Message-ID: <BEE28BF86078B6429D6C780635718E210395E8@morelia.be.devgen.com>



> -----Original Message-----
> From: Stefanie Lager [mailto:stefanielager at fastmail.ca]
> Sent: vrijdag 13 februari 2004 9:53
> To: emboss at embnet.org
> Subject: RE: [EMBOSS] Database access external app
> 
> 
> Marc,
> 
> I use the same setup as you "app: "fastacmd -d hs_pub_genomic -s %s",
> and I try to retrive from a human genome database (each chr is a BIG
> fasta file). The formatdb indexing seems OK, fastacmd works on
> commandline. But I don't get any error from EMBOSS it just 
> can't retrive
> entries (it just hangs there forever). 

Hey, now you mention it ! We also have this on another machine where EMBOSS 2.8.0 is installed.
Also there it hangs when an external application should fetch the entry (from a database).
We don't have a problem on the other machines where EMBOSS 2.7.1 is installed.
So there might be an issue after all ??
Marc


From pmr at ebi.ac.uk  Fri Feb 13 04:52:02 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 13 Feb 2004 09:52:02 +0000
Subject: [EMBOSS] Database access external app
In-Reply-To: <20040213085320.4F6E7863CFF@mail.interchange.ca>
References: <20040213085320.4F6E7863CFF@mail.interchange.ca>
Message-ID: <402C9E42.1070105@ebi.ac.uk>

Stefanie Lager wrote:

> Marc,
> 
> I use the same setup as you "app: "fastacmd -d hs_pub_genomic -s %s",
> and I try to retrive from a human genome database (each chr is a BIG
> fasta file). The formatdb indexing seems OK, fastacmd works on
> commandline. But I don't get any error from EMBOSS it just can't retrive
> entries (it just hangs there forever). 

The hang is a known problem to be fixed in 2.8.1 - entries over a 
certain size will hang in 2.8.0 because we added a wait loop to catch 
zombie processes.

As a quick fix (patch version of ajfile.c to be added to the FTP 
server), you can:

edit ajax/ajfile.c

in function ajFileNewInPipe, remove this loop at the end of the function:

     ret = -1;
     while(ret != pid)
     {
         ret = wait(&status);
         if(ret == -1)
             if(ret != EINTR)
                 ret = pid;
     }

Then make (and make install if you installed EMBOSS)

This loop will hang if the external process has unread data. (The real 
fix is to move this loop to the file close functions)

Hope this helps,

Peter Rice



From stefanielager at fastmail.ca  Fri Feb 13 06:44:39 2004
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Fri, 13 Feb 2004 11:44:39 +0000 (UTC)
Subject: [EMBOSS] Database access external app
In-Reply-To: <402CA024.4060704@ebi.ac.uk>
Message-ID: <20040213114440.C6B7E861214@mail.interchange.ca>

Thank you Peter,

Changing the ajfile.c file solved the problem, and YES i do run EMBOSS
2.8.0.

Stefanie

> 
> Because the ajfile.c fix only affects sequences above a certain size,
> most protein and gene sequences in FASTA format will be too short to
> hang.
> 
> Try the ajfile.c fix ... I expect it will fix your "fastacmd problem".
> 
> If you still have problems, let me know.
> 
> regards,
> 
> Peter Rice
> 
_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians


From gbottu at ben.vub.ac.be  Fri Feb 13 15:15:46 2004
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Fri, 13 Feb 2004 21:15:46 +0100
Subject: [EMBOSS] Staden and EMBOSS 2.8.O
Message-ID: <20040213201546.GA29575@bigben.ulb.ac.be>

	Dear colleagues,

As you all know, with EMBOSS 2.8.O the syntax of the ACD files has 
changed. An unfortunate consequence is that EMBOSS programs do not work 
well or not at all anymore under Staden spin or spin2. The script 
acd2tcl.tcl should be updated as to handle new things like the rename 
required -> standard and the use of $acdprotein. Unfortunately there is no 
support for Staden anymore (well, it was recently announced that James 
Bonfield is working at Sanger Centre, but according to the Web page he is 
only developing gap4, not spin). Does someone know more about it ?

	Guy Bottu,
	BEN


From humberto at hpcf.upr.edu  Fri Feb 13 21:17:30 2004
From: humberto at hpcf.upr.edu (Humberto Ortiz Zuazaga)
Date: Fri, 13 Feb 2004 22:17:30 -0400
Subject: [EMBOSS] bioknoppix: a linux live CD with EMBOSS
Message-ID: <20040213221730.323520d7.humberto@hpcf.upr.edu>

Carlos Rodriguez and I have put together a custom KNOPPIX CD with
several bioinformatics applicacions. I'm using it to teach a
bioinformatics course at the University of Puerto Rico. The students can
take the whole course environment back to their labs, or home to
practice.

You can get the CD images from:

http://bioknoppix.hpcf.upr.edu/

The CD boots into a graphical KDE environment, with EMBOSS 2.8.0
installed, as well as ImageJ, bioconductor, R, Cn3D, rasmol, Artemis. We
also included jemboss standalone, but this release has a bug in the
jemboss installation. 

The t* databases are installed, so students can follow the tutorial or
program manual examples for EMBOSS.

This version also includes SRS access to embl, genbank, swissprot, pir
via srswww to Sanger and Indiana University.

Please download the CD images and let us know how we can improve the
system.

-- 
Humberto Ortiz-Zuazaga
Carlos Rodriguez
High Performance Computing facility
University of Puerto Rico
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From sbassi at telefax.com.ar  Fri Feb 13 22:49:15 2004
From: sbassi at telefax.com.ar (Sebastian Bassi)
Date: Sat, 14 Feb 2004 00:49:15 -0300
Subject: [EMBOSS] Linux for bioinformatics: Name change. BioShell now is DNALinux
Message-ID: <402D9ABB.5030404@telefax.com.ar>

About a month ago I posted an announce regarding Bioshell. A Linux 
distro based on a LiveCD (Slax). Thank to people at IGH and Quilmes 
National University, I put it online.
Here is the official announce:


(Quilmes, Argentina). GenesDigitales is releasing the first public 
version of a linux distribution oriented toward life science users: 
DNALinux 0.13.
     It is based on a reduced version of Slackware Linux (Slax) with 
bioinformatic software and genome data included. One key feature of 
DNALinux is that works as a LiveCD, that is, without making any 
permanent change on the hard disk. The distro could be tested or used 
without any risk of data loss. It also could be installed as a regular 
Linux if you want (check the FAQ at www.dnalinux.com for details).
     Here is the list of bioinformatics programs:

BLAST
EMBOSS-2.8.0
T-COFFEE_distribution_Version_1.37
abacus-0.63
arka-0.11
avid
big_mac
cap3
clustalx1.81.linux
e-pcr
efmc
hmmer-2.3.2.bin.intel-linux
ncbi
paml3.12
primer3_0_9_test

     Sequence data included (on BLAST format):

Arabidopsis Thaliana (aa).
Drosophila Malanogaster (aa)
Escherichia Coli (aa).

     This is a fist release, so there is a lot of things to improve. We 
are working in the next major release, set for April/May 2004. If you 
want to check this version, please take a look at www.dnalinux.com, 
where you could download DNALinux (free registration requiered).

DNALinux team at GenesDigitales: info at genesdigitales.com

                 http://Bioinformatica.info



From sbassi at telefax.com.ar  Fri Feb 13 22:58:11 2004
From: sbassi at telefax.com.ar (Sebastian Bassi)
Date: Sat, 14 Feb 2004 00:58:11 -0300
Subject: [EMBOSS] bioknoppix: a linux live CD with EMBOSS
In-Reply-To: <20040213221730.323520d7.humberto@hpcf.upr.edu>
References: <20040213221730.323520d7.humberto@hpcf.upr.edu>
Message-ID: <402D9CD3.3050509@telefax.com.ar>

Humberto Ortiz Zuazaga wrote:

> Carlos Rodriguez and I have put together a custom KNOPPIX CD with
> several bioinformatics applicacions. I'm using it to teach a
> bioinformatics course at the University of Puerto Rico. The students can
> take the whole course environment back to their labs, or home to
> practice.

Seems we are all with the same idea!.
Bioinformatics.org is hosting even another project with similar goals 
(Bio-Linux, look at http://envgen.nox.ac.uk/biolinux.html) they are 
based in RedHat but they are considering Debian/Knoppix.
I fell like making redundant work :)



From kawaji at unza.org  Sun Feb 15 11:33:39 2004
From: kawaji at unza.org (KAWAJI Hideya)
Date: Mon, 16 Feb 2004 01:33:39 +0900 (JST)
Subject: [EMBOSS] Tutorial translation into Japanese
Message-ID: <20040216.013339.907658695.kawaji@unza.org>

Hi,

We, JAMBO (Japan EMBOSS Users Group), release the translation
of the EMBOSS tutorial into Japanese. Just a section, 'Preface from translators'
(http://transgenic.cats.st/jambo/doc/tutorial_jp/node1.html)
are added, and the contributers are listed there in English and Japanese.

It is very honor if our translation is sited by the EMBOSS site,
or included by the EMBOSS package.


  [Wiki]
  http://transgenic.cats.st/jambo/index.php?%5B%5BEMBOSS%A4%F2%CD%D1%A4%A4%A4%BF%C7%DB%CE%F3%B2%F2%C0%CF%A4%D8%A4%CE%BC%EA%B0%FA%A4%AD%5D%5D

  [Archive of LaTeX source, PS ver., PDF ver.]
  http://transgenic.cats.st/jambo/doc/tutorial_jp/emboss_tutorial_ja.Release1.zip

  [HTML ver.]
  http://transgenic.cats.st/jambo/doc/tutorial_jp/index.html

  [Archive of HTML ver.]
http://transgenic.cats.st/jambo/doc/tutorial_jp/emboss_tutorial_ja_html.Release1.zip

  [PDF ver.]
  http://transgenic.cats.st/jambo/doc/tutorial_jp/emboss_tutorial_ja.pdf


Best regards,
---
Hideya KAWAJI <kawaji at unza.org>  # My e-mail address has been changed


From simon.andrews at bbsrc.ac.uk  Mon Feb 16 03:19:33 2004
From: simon.andrews at bbsrc.ac.uk (simon andrews (BI))
Date: Mon, 16 Feb 2004 08:19:33 -0000
Subject: [EMBOSS] Staden and EMBOSS 2.8.O
Message-ID: <2DC41140A89ED411989D00508BDCD9ED01E28CD0@bi-exsrv1.iapc.bbsrc.ac.uk>



> -----Original Message-----
> From: Guy Bottu [mailto:gbottu at ben.vub.ac.be] 
> Subject: [EMBOSS] Staden and EMBOSS 2.8.O
> 
> Unfortunately there is no support for Staden anymore (well, 
> it was recently announced that James Bonfield is working 
> at Sanger Centre, but according to the Web page he is 
> only developing gap4, not spin). Does someone know more about it ?

James recently announced that the MRC have finally agreed to release Staden under an opensource licence.  It is therefore now being hosted and developed as a sourceforge project:

http://staden.sourceforge.net/

https://sourceforge.net/projects/staden

..therefore if you're up to making the changes yourself you can submit patches to the project, or if not you can file it as a bug which someone else will hopefully pick up.

Simon.


From kawaji at unza.org  Mon Feb 16 09:48:49 2004
From: kawaji at unza.org (KAWAJI Hideya)
Date: Mon, 16 Feb 2004 23:48:49 +0900 (JST)
Subject: [EMBOSS] Re: Tutorial translation into Japanese
In-Reply-To: <20040216.013339.907658695.kawaji@unza.org>
References: <20040216.013339.907658695.kawaji@unza.org>
Message-ID: <20040216.234849.373533604.kawaji@unza.org>

Hi, 


In my translation into Japanese, I found just a small point to be corrected
in the EMBOSS tutorial.

It's in the chapter 'Working with sequences'. 
http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Doc/Tutorial/emboss_tutorial/node2.html

Although 'seqretallfeat' is mentioned to retrieve all features,
it has been integrated into 'seqret', due to version up.
It should be replaced by 'seqret -feature' for current version.

best,
---
Hideya KAWAJI <kawaji at unza.org>


From m.claesson at student.ucc.ie  Tue Feb 17 05:58:29 2004
From: m.claesson at student.ucc.ie (Marcus Claesson)
Date: 17 Feb 2004 10:58:29 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
Message-ID: <1077015509.5582.15.camel@morpheus.ucc.ie>

Hello,

I have a silly little problem indexing databases in Emboss-2.8.0. After
running dbifasta and adding DB entries in emboss.default I can only
access the database when being in the same directory as the fasta file.
Here is what I did:

[blast_db]$ uname -a
Linux neo.ucc.ie 2.4.9-e.35enterprise #1 SMP Tue Dec 23 00:06:16 EST
2003 i686 unknown

[blast_db]$ pwd
/var/data/blast_db

[blast_db]$ ll ecoli.nt
-rw-r--r--    1 marcus   bioinfo   4763013 Jan 15 01:38 ecoli.nt

[blast_db]$ dbifasta
Index a fasta database
    simple : >ID
     idacc : >ID ACC
     gcgid : >db:ID
  gcgidacc : >db:ID ACC
      dbid : >db ID
      ncbi : | formats
ID line format [idacc]: 
Database directory [.]: /var/data/blast_db
Wildcard database filename [*.dat]: ecoli.nt
Database name: ecoli.nt
Release number [0.0]: 
Index date [00/00/00]:

[blast_db]$ ll entrynam.idx division.lkp acnum.*
-rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 acnum.hit
-rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 acnum.trg
-rw-rw-r--    1 marcus   bioinfo       330 Feb 17 10:39 division.lkp
-rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 entrynam.idx

Added these lines in /usr/local/EMBOSS-2.8.0/emboss/emboss.default:

DB ecoli.nt [
   type: "N"
   format: "fasta"
   method: "emblcd"
   dir: "/var/data/blast_db/"
]

[blast_db]$ showdb
Displays information on the currently available databases
# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
ecoli.nt      N    OK  OK  OK  -

[blast_db]$ cd ~

[marcus]$ seqret ecoli.nt
Reads and writes (returns) sequences
Error: failed to open filename 'ecoli.nt'
Error: Unable to read sequence 'ecoli.nt'
Died: seqret terminated: Bad value for '-sequence' and no prompt

But it works when I'm the same directory as ecoli.nt:

[blast_db]$  seqret ecoli.nt
Reads and writes (returns) sequences
Output sequence [ae000111.fasta]: 
etc...

Clearly it must be possible to access ecoli.nt from other directories?


Extremly grateful for any help on this!

Regards,
Marcus





From MAILER-DAEMON at pool.informatik.rwth-aachen.de  Tue Feb 17 08:33:48 2004
From: MAILER-DAEMON at pool.informatik.rwth-aachen.de (Mail Delivery System)
Date: Tue, 17 Feb 2004 14:33:48 +0100 (CET)
Subject: [EMBOSS] Undelivered Mail Returned to Sender
Message-ID: <20040217133348.3573AA8CF@poolmail.informatik.rwth-aachen.de>

This is the Postfix program at host poolmail.informatik.rwth-aachen.de.

I'm sorry to have to inform you that the message returned
below could not be delivered to one or more destinations.

For further assistance, please send mail to <postmaster>

If you do so, please include this problem report. You can
delete your own text from the message returned below.

			The Postfix program

<maria at pool.informatik.rwth-aachen.de>: unknown user: "maria"
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From jlaroche at bioinfo.ulaval.ca  Tue Feb 17 08:57:51 2004
From: jlaroche at bioinfo.ulaval.ca (=?ISO-8859-1?Q?J=E9r=F4me_Laroche?=)
Date: Tue, 17 Feb 2004 08:57:51 -0500
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <1077015509.5582.15.camel@morpheus.ucc.ie>
References: <1077015509.5582.15.camel@morpheus.ucc.ie>
Message-ID: <46996444-6151-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>

Hi Marcus,

  it seems that your file .emboss_default don't have the line to specify 
the location of the indexed database (check the last line of my 
example).
Also, you can add this line at the begining of your file (setting a 
variable for the path of your database) so if you move your database 
and your index, you just have to modify the path at this line.



SET jerome_database_dir /cbi/people/jlaroche/data/banquesemboss


DB rbcl [
    type: N
    method: emblcd
    format: fasta
    dir: $jerome_database_dir/banque1
    indexdir: $jerome_database_dir/banque1
]



Jerome

Centre de bioinformatique
Pavillon Charles-Eug?ne-Marchand
Bureau 4233d
t?l: 418-656-2131 poste 6184
fax: 418-656-7176
www.bioinfo.ulaval.ca


Le 04-02-17, ? 05:58, Marcus Claesson a ?crit :

> Hello,
>
> I have a silly little problem indexing databases in Emboss-2.8.0. After
> running dbifasta and adding DB entries in emboss.default I can only
> access the database when being in the same directory as the fasta file.
> Here is what I did:
>
> [blast_db]$ uname -a
> Linux neo.ucc.ie 2.4.9-e.35enterprise #1 SMP Tue Dec 23 00:06:16 EST
> 2003 i686 unknown
>
> [blast_db]$ pwd
> /var/data/blast_db
>
> [blast_db]$ ll ecoli.nt
> -rw-r--r--    1 marcus   bioinfo   4763013 Jan 15 01:38 ecoli.nt
>
> [blast_db]$ dbifasta
> Index a fasta database
>     simple : >ID
>      idacc : >ID ACC
>      gcgid : >db:ID
>   gcgidacc : >db:ID ACC
>       dbid : >db ID
>       ncbi : | formats
> ID line format [idacc]:
> Database directory [.]: /var/data/blast_db
> Wildcard database filename [*.dat]: ecoli.nt
> Database name: ecoli.nt
> Release number [0.0]:
> Index date [00/00/00]:
>
> [blast_db]$ ll entrynam.idx division.lkp acnum.*
> -rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 acnum.hit
> -rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 acnum.trg
> -rw-rw-r--    1 marcus   bioinfo       330 Feb 17 10:39 division.lkp
> -rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 entrynam.idx
>
> Added these lines in /usr/local/EMBOSS-2.8.0/emboss/emboss.default:
>
> DB ecoli.nt [
>    type: "N"
>    format: "fasta"
>    method: "emblcd"
>    dir: "/var/data/blast_db/"
> ]
>
> [blast_db]$ showdb
> Displays information on the currently available databases
> # Name        Type ID  Qry All Comment
> # ====        ==== ==  === === =======
> ecoli.nt      N    OK  OK  OK  -
>
> [blast_db]$ cd ~
>
> [marcus]$ seqret ecoli.nt
> Reads and writes (returns) sequences
> Error: failed to open filename 'ecoli.nt'
> Error: Unable to read sequence 'ecoli.nt'
> Died: seqret terminated: Bad value for '-sequence' and no prompt
>
> But it works when I'm the same directory as ecoli.nt:
>
> [blast_db]$  seqret ecoli.nt
> Reads and writes (returns) sequences
> Output sequence [ae000111.fasta]:
> etc...
>
> Clearly it must be possible to access ecoli.nt from other directories?
>
>
> Extremly grateful for any help on this!
>
> Regards,
> Marcus
>
>



From m.claesson at student.ucc.ie  Tue Feb 17 09:49:47 2004
From: m.claesson at student.ucc.ie (Marcus Claesson)
Date: 17 Feb 2004 14:49:47 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <46996444-6151-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
References: <1077015509.5582.15.camel@morpheus.ucc.ie>
	 <46996444-6151-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
Message-ID: <1077029387.5582.24.camel@morpheus.ucc.ie>

Thanks for your answer Jerome! But it didn't seem to help me. I added
the indexdir line with the same path (where the index files and fasta
file is) as "dir:". I tried this both with and without setting a
emboss_db_dir variable, but it still didn't work. In other words I can
still only access the database (that shows up in showdb) if I am in that
fasta file directory.

Do I need to set this path somewhere else than in emboss.default you
think?

Marcus



On Tue, 2004-02-17 at 13:57, J?r?me Laroche wrote:
> Hi Marcus,
> 
>   it seems that your file .emboss_default don't have the line to specify 
> the location of the indexed database (check the last line of my 
> example).
> Also, you can add this line at the begining of your file (setting a 
> variable for the path of your database) so if you move your database 
> and your index, you just have to modify the path at this line.
> 
> 
> 
> SET jerome_database_dir /cbi/people/jlaroche/data/banquesemboss
> 
> 
> DB rbcl [
>     type: N
>     method: emblcd
>     format: fasta
>     dir: $jerome_database_dir/banque1
>     indexdir: $jerome_database_dir/banque1
> ]
> 
> 
> 
> Jerome
> 
> Centre de bioinformatique
> Pavillon Charles-Eug?ne-Marchand
> Bureau 4233d
> t?l: 418-656-2131 poste 6184
> fax: 418-656-7176
> www.bioinfo.ulaval.ca
> 
> 
> Le 04-02-17, ? 05:58, Marcus Claesson a ?crit :
> 
> > Hello,
> >
> > I have a silly little problem indexing databases in Emboss-2.8.0. After
> > running dbifasta and adding DB entries in emboss.default I can only
> > access the database when being in the same directory as the fasta file.
> > Here is what I did:
> >
> > [blast_db]$ uname -a
> > Linux neo.ucc.ie 2.4.9-e.35enterprise #1 SMP Tue Dec 23 00:06:16 EST
> > 2003 i686 unknown
> >
> > [blast_db]$ pwd
> > /var/data/blast_db
> >
> > [blast_db]$ ll ecoli.nt
> > -rw-r--r--    1 marcus   bioinfo   4763013 Jan 15 01:38 ecoli.nt
> >
> > [blast_db]$ dbifasta
> > Index a fasta database
> >     simple : >ID
> >      idacc : >ID ACC
> >      gcgid : >db:ID
> >   gcgidacc : >db:ID ACC
> >       dbid : >db ID
> >       ncbi : | formats
> > ID line format [idacc]:
> > Database directory [.]: /var/data/blast_db
> > Wildcard database filename [*.dat]: ecoli.nt
> > Database name: ecoli.nt
> > Release number [0.0]:
> > Index date [00/00/00]:
> >
> > [blast_db]$ ll entrynam.idx division.lkp acnum.*
> > -rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 acnum.hit
> > -rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 acnum.trg
> > -rw-rw-r--    1 marcus   bioinfo       330 Feb 17 10:39 division.lkp
> > -rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 entrynam.idx
> >
> > Added these lines in /usr/local/EMBOSS-2.8.0/emboss/emboss.default:
> >
> > DB ecoli.nt [
> >    type: "N"
> >    format: "fasta"
> >    method: "emblcd"
> >    dir: "/var/data/blast_db/"
> > ]
> >
> > [blast_db]$ showdb
> > Displays information on the currently available databases
> > # Name        Type ID  Qry All Comment
> > # ====        ==== ==  === === =======
> > ecoli.nt      N    OK  OK  OK  -
> >
> > [blast_db]$ cd ~
> >
> > [marcus]$ seqret ecoli.nt
> > Reads and writes (returns) sequences
> > Error: failed to open filename 'ecoli.nt'
> > Error: Unable to read sequence 'ecoli.nt'
> > Died: seqret terminated: Bad value for '-sequence' and no prompt
> >
> > But it works when I'm the same directory as ecoli.nt:
> >
> > [blast_db]$  seqret ecoli.nt
> > Reads and writes (returns) sequences
> > Output sequence [ae000111.fasta]:
> > etc...
> >
> > Clearly it must be possible to access ecoli.nt from other directories?
> >
> >
> > Extremly grateful for any help on this!
> >
> > Regards,
> > Marcus
> >
> >
> 



From m.claesson at student.ucc.ie  Tue Feb 17 10:23:32 2004
From: m.claesson at student.ucc.ie (Marcus Claesson)
Date: 17 Feb 2004 15:23:32 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <BC57DECC.DA37%d.m.a.martin@dundee.ac.uk>
References: <BC57DECC.DA37%d.m.a.martin@dundee.ac.uk>
Message-ID: <1077031412.5582.32.camel@morpheus.ucc.ie>

Hi,

I have now changed emboss/emboss.defaults to:

SET $emboss_db_dir /var/data/blast_db

DB ecoli.nt [
   type: "N"
   format: "fasta"
   method: "emblcd"
   dir: "$emboss_db_dir"
   indexdir: "$emboss_db_dir"
   file: "ecoli.nt"
]

And get the same negative result:

[marcus]$ showdb
Displays information on the currently available databases
# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
ecoli.nt      N    OK  OK  OK  -

[marcus]$ seqret ecoli.nt
Reads and writes (returns) sequences
Error: failed to open filename 'ecoli.nt'
Error: Unable to read sequence 'ecoli.nt'
Died: seqret terminated: Bad value for '-sequence' and no prompt

I find this very strange! If you don't know what's wrong would you know
anywhere else I can get help with this?

Thanks again.

Marcus


On Tue, 2004-02-17 at 15:07, David Martin wrote:
> On 17/2/04 2:49 pm, "Marcus Claesson" <m.claesson at student.ucc.ie> wrote:
> 
> > Thanks for your answer Jerome! But it didn't seem to help me. I added
> > the indexdir line with the same path (where the index files and fasta
> > file is) as "dir:". I tried this both with and without setting a
> > emboss_db_dir variable, but it still didn't work. In other words I can
> > still only access the database (that shows up in showdb) if I am in that
> > fasta file directory.
> 
> This is because you have not set the file: option? try that and see if it
> works.
> in the original example you give the database the same name as the fasta
> file so it works if it is in the right directory.
> 
> > 
> > Do I need to set this path somewhere else than in emboss.default you
> > think?
> 
> >> SET jerome_database_dir /cbi/people/jlaroche/data/banquesemboss
> >> 
> >> 
> >> DB rbcl [
> >>     type: N
> >>     method: emblcd
> >>     format: fasta
> >>     dir: $jerome_database_dir/banque1
> >>     indexdir: $jerome_database_dir/banque1
>        file: seqfile.fasta
>        comment: "It is useful to put a description here"
> >> ]
> 
> 
> ..d



From d.m.a.martin at dundee.ac.uk  Tue Feb 17 10:28:42 2004
From: d.m.a.martin at dundee.ac.uk (David Martin)
Date: Tue, 17 Feb 2004 15:28:42 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <1077031412.5582.32.camel@morpheus.ucc.ie>
Message-ID: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk>

On 17/2/04 3:23 pm, "Marcus Claesson" <m.claesson at student.ucc.ie> wrote:

> Hi,
> 
> I have now changed emboss/emboss.defaults to:
> 
> SET $emboss_db_dir /var/data/blast_db
> 
> DB ecoli.nt [
>  type: "N"
>  format: "fasta"
>  method: "emblcd"
>  dir: "$emboss_db_dir"
>  indexdir: "$emboss_db_dir"
>  file: "ecoli.nt"
> ]
> 
> And get the same negative result:
> 
> [marcus]$ showdb
> Displays information on the currently available databases
> # Name        Type ID  Qry All Comment
> # ====        ==== ==  === === =======
> ecoli.nt      N    OK  OK  OK  -
> 
> [marcus]$ seqret ecoli.nt

'seqret ecoli.nt:\*' perhaps?

..d

> Reads and writes (returns) sequences
> Error: failed to open filename 'ecoli.nt'
> Error: Unable to read sequence 'ecoli.nt'
> Died: seqret terminated: Bad value for '-sequence' and no prompt
> 
> I find this very strange! If you don't know what's wrong would you know
> anywhere else I can get help with this?
> 
> Thanks again.
> 
> Marcus
> 
> 
> On Tue, 2004-02-17 at 15:07, David Martin wrote:
>> On 17/2/04 2:49 pm, "Marcus Claesson" <m.claesson at student.ucc.ie> wrote:
>> 
>>> Thanks for your answer Jerome! But it didn't seem to help me. I added
>>> the indexdir line with the same path (where the index files and fasta
>>> file is) as "dir:". I tried this both with and without setting a
>>> emboss_db_dir variable, but it still didn't work. In other words I can
>>> still only access the database (that shows up in showdb) if I am in that
>>> fasta file directory.
>> 
>> This is because you have not set the file: option? try that and see if it
>> works.
>> in the original example you give the database the same name as the fasta
>> file so it works if it is in the right directory.
>> 
>>> 
>>> Do I need to set this path somewhere else than in emboss.default you
>>> think?
>> 
>>>> SET jerome_database_dir /cbi/people/jlaroche/data/banquesemboss
>>>> 
>>>> 
>>>> DB rbcl [
>>>>     type: N
>>>>     method: emblcd
>>>>     format: fasta
>>>>     dir: $jerome_database_dir/banque1
>>>>     indexdir: $jerome_database_dir/banque1
>>        file: seqfile.fasta
>>        comment: "It is useful to put a description here"
>>>> ]
>> 
>> 
>> ..d
> 
> 



From gwilliam at hgmp.mrc.ac.uk  Tue Feb 17 10:31:08 2004
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Tue, 17 Feb 2004 15:31:08 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
References: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk>
Message-ID: <403233BC.BD3BF7C4@hgmp.mrc.ac.uk>

David Martin wrote:
> 
> On 17/2/04 3:23 pm, "Marcus Claesson" <m.claesson at student.ucc.ie> wrote:
> 
> > Hi,
> >
> > I have now changed emboss/emboss.defaults to:
> >
> > SET $emboss_db_dir /var/data/blast_db
> >
> > DB ecoli.nt [
> >  type: "N"
> >  format: "fasta"
> >  method: "emblcd"
> >  dir: "$emboss_db_dir"
> >  indexdir: "$emboss_db_dir"
> >  file: "ecoli.nt"
> > ]
> >
> > And get the same negative result:
> >
> > [marcus]$ showdb
> > Displays information on the currently available databases
> > # Name        Type ID  Qry All Comment
> > # ====        ==== ==  === === =======
> > ecoli.nt      N    OK  OK  OK  -
> >
> > [marcus]$ seqret ecoli.nt
> 
> 'seqret ecoli.nt:\*' perhaps?

That would be more explicit and clearer for other people to read, but a
database-name on its own is a perfectly legal EMBOSS USA.

Try: 'seqret embl'

-- 
Gary Williams
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494522			Fax: +44 1223 494512
E-mail: gwilliam at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk


From Marc.Logghe at devgen.com  Tue Feb 17 10:32:10 2004
From: Marc.Logghe at devgen.com (Marc Logghe)
Date: Tue, 17 Feb 2004 16:32:10 +0100
Subject: [EMBOSS] can't access databases indexed by dbifasta
Message-ID: <BEE28BF86078B6429D6C780635718E21904B9A@morelia.be.devgen.com>

Hi,
Reminds me of a problem I had a while ago. Maybe it is a similar problem. Have a look at: http://www.hgmp.mrc.ac.uk/Emboss/HYPERMAIL/emboss/emboss.200305/0008.html
HTH,
Marc

> -----Original Message-----
> From: Marcus Claesson [mailto:m.claesson at student.ucc.ie]
> Sent: dinsdag 17 februari 2004 16:24
> To: David Martin
> Cc: emboss at embnet.org
> Subject: Re: [EMBOSS] can't access databases indexed by dbifasta
> 
> 
> Hi,
> 
> I have now changed emboss/emboss.defaults to:
> 
> SET $emboss_db_dir /var/data/blast_db
> 
> DB ecoli.nt [
>    type: "N"
>    format: "fasta"
>    method: "emblcd"
>    dir: "$emboss_db_dir"
>    indexdir: "$emboss_db_dir"
>    file: "ecoli.nt"
> ]
> 
> And get the same negative result:
> 
> [marcus]$ showdb
> Displays information on the currently available databases
> # Name        Type ID  Qry All Comment
> # ====        ==== ==  === === =======
> ecoli.nt      N    OK  OK  OK  -
> 
> [marcus]$ seqret ecoli.nt
> Reads and writes (returns) sequences
> Error: failed to open filename 'ecoli.nt'
> Error: Unable to read sequence 'ecoli.nt'
> Died: seqret terminated: Bad value for '-sequence' and no prompt
> 
> I find this very strange! If you don't know what's wrong 
> would you know
> anywhere else I can get help with this?
> 
> Thanks again.
> 
> Marcus
> 
> 
> On Tue, 2004-02-17 at 15:07, David Martin wrote:
> > On 17/2/04 2:49 pm, "Marcus Claesson" 
> <m.claesson at student.ucc.ie> wrote:
> > 
> > > Thanks for your answer Jerome! But it didn't seem to help 
> me. I added
> > > the indexdir line with the same path (where the index 
> files and fasta
> > > file is) as "dir:". I tried this both with and without setting a
> > > emboss_db_dir variable, but it still didn't work. In 
> other words I can
> > > still only access the database (that shows up in showdb) 
> if I am in that
> > > fasta file directory.
> > 
> > This is because you have not set the file: option? try that 
> and see if it
> > works.
> > in the original example you give the database the same name 
> as the fasta
> > file so it works if it is in the right directory.
> > 
> > > 
> > > Do I need to set this path somewhere else than in 
> emboss.default you
> > > think?
> > 
> > >> SET jerome_database_dir /cbi/people/jlaroche/data/banquesemboss
> > >> 
> > >> 
> > >> DB rbcl [
> > >>     type: N
> > >>     method: emblcd
> > >>     format: fasta
> > >>     dir: $jerome_database_dir/banque1
> > >>     indexdir: $jerome_database_dir/banque1
> >        file: seqfile.fasta
> >        comment: "It is useful to put a description here"
> > >> ]
> > 
> > 
> > ..d
> 
> 


From m.claesson at student.ucc.ie  Tue Feb 17 10:41:02 2004
From: m.claesson at student.ucc.ie (Marcus Claesson)
Date: 17 Feb 2004 15:41:02 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk>
References: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk>
Message-ID: <1077032461.5582.34.camel@morpheus.ucc.ie>


> 'seqret ecoli.nt:\*' perhaps?

Nope, same bad result...

/M



From jlaroche at bioinfo.ulaval.ca  Tue Feb 17 10:50:16 2004
From: jlaroche at bioinfo.ulaval.ca (=?ISO-8859-1?Q?J=E9r=F4me_Laroche?=)
Date: Tue, 17 Feb 2004 10:50:16 -0500
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <1077032461.5582.34.camel@morpheus.ucc.ie>
References: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk> <1077032461.5582.34.camel@morpheus.ucc.ie>
Message-ID: <FB53EFC8-6160-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>

Marcus,

as suggested earlier by David, take a different name for your database. 
Take only ecoli or something else. I try this with my data and I got 
the same problem.


Jerome

Centre de bioinformatique
Pavillon Charles-Eug?ne-Marchand
Bureau 4233d
t?l: 418-656-2131 poste 6184
fax: 418-656-7176
www.bioinfo.ulaval.ca
Le 04-02-17, ? 10:41, Marcus Claesson a ?crit :

>
>> 'seqret ecoli.nt:\*' perhaps?
>
> Nope, same bad result...
>
> /M
>



From m.claesson at student.ucc.ie  Wed Feb 18 08:40:43 2004
From: m.claesson at student.ucc.ie (Marcus Claesson)
Date: 18 Feb 2004 13:40:43 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <11B65834-6169-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
References: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk>
	 <1077032461.5582.34.camel@morpheus.ucc.ie>
	 <FB53EFC8-6160-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
	 <1077035334.5582.38.camel@morpheus.ucc.ie>
	 <11B65834-6169-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
Message-ID: <1077111643.25361.59.camel@morpheus.ucc.ie>

I entered a 'field' in both dbifasta and emboss.defaults and it works
now! This is what I did (I have one last tiny question in the end):

[blast_db]$ dbifasta -fields des
Index a fasta database
    simple : >ID
     idacc : >ID ACC
     gcgid : >db:ID
  gcgidacc : >db:ID ACC
      dbid : >db ID
      ncbi : | formats
ID line format [idacc]: ncbi
Database directory [.]: 
Wildcard database filename [*.dat]: ecoli.nt
Database name: ecoli_nt
Release number [0.0]: 
Index date [00/00/00]:

in emboss/emboss.defaults:
DB ecoli_nt [
   type: N
   format: fasta
   method: emblcd
   dir: 
   indexdir: 
   file: ecoli.nt
   fields: des
]

[blast_db]$ showdb
Displays information on the currently available databases
# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
ecoli_nt      N    OK  OK  OK  -


Now this works:
[marcus]$ seqret ecoli_nt:NC_0012\*
>NC_001224.1 NC_001224.1 Saccharomyces cerevisiae mitochondrion,
complete genome
TTCATAATTAATTTTTTATATATATATTATATTATAATATTAATTTATATTATAAAAATA
ATATTTATTATTAAAATATTTATTCTCCTTTCGGGGTTCCGGCTCCCGTGGCCGGGCCCC
GGAATTATTAATTAATAATAAATTATTATTAATAATTATTTATTATTTTAT


But this doesn't work and I don't know why since I added the 'des
field'. Are queries like these suppose to work by the way?

[marcus]$ seqret ecoli_nt:\*mitochondrio\* -auto -stdout
Error: Unable to read sequence 'ecoli_nt:*mitochondrio*'
Died: seqret terminated: Bad value for '-sequence' with -auto defined


Thanks for all help so far!

Marcus






On Tue, 2004-02-17 at 16:48, J?r?me Laroche wrote:
> Marcus,
> 
> which one is the right? Because in the first, at the question "Wildcard 
> database filename:" you enter only ecoli and I think that your sequence 
> file is ecoli.nt It is only at the line "Database name:" that you enter 
> the name ecoli (without the nt). If it doesn't work, check again your 
> emboss_default file and ensure you have the requested field for your 
> database and your index and the right syntax for the location of your 
> file.
> 
> Finally, reply to all, for all the people know what is the right thing 
> to do in that case.
> 
> 
> Good luck!
> 
> Jerome
> 
> 
> > This is how I created it:
> > [blast_db]$ dbifasta
> > Index a fasta database
> >     simple : >ID
> >      idacc : >ID ACC
> >      gcgid : >db:ID
> >   gcgidacc : >db:ID ACC
> >       dbid : >db ID
> >       ncbi : | formats
> > ID line format [idacc]:
> > Database directory [.]: /var/data/blast_db
> > Wildcard database filename [*.dat]: ecoli
> > Database name: ecoli
> >
> 
> > [marcus at neo blast_db]$ dbifasta
> > Index a fasta database
> >     simple : >ID
> >      idacc : >ID ACC
> >      gcgid : >db:ID
> >   gcgidacc : >db:ID ACC
> >       dbid : >db ID
> >       ncbi : | formats
> > ID line format [idacc]:
> > Database directory [.]: /var/data/blast_db
> > Wildcard database filename [*.dat]: ecoli.nt
> > Database name: ecoli
> > Release number [0.0]:
> > Index date [00/00/00]:
> 
> 
> 
> Jerome
> 
> Centre de bioinformatique
> Pavillon Charles-Eug?ne-Marchand
> Bureau 4233d
> t?l: 418-656-2131 poste 6184
> fax: 418-656-7176
> www.bioinfo.ulaval.ca
> Le 04-02-17, ? 11:29, Marcus Claesson a ?crit :
> 
> > Thanks Jerome it works! However there is one thing I don't understand
> > (or I just misunderstood the syntax)...
> >
> > This happens when I want a certain entry from this new ecoli db:
> >
> > [marcus]$ seqret ecoli:AE00011\* -stdout -auto
> > Error: Unable to read sequence 'ecoli:AE00011*'
> > Died: seqret terminated: Bad value for '-sequence' with -auto defined
> >
> > The entry looks like:
> > [marcus]$ seqret ecoli -stdout -auto |head
> >> AE000111 AE000111.1 Escherichia coli K-12 MG1655 section 1 of 400 of
> > the complete geno
> > me
> > AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
> > TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTT
> >
> >
> > This is how I created it:
> > [blast_db]$ dbifasta
> > Index a fasta database
> >     simple : >ID
> >      idacc : >ID ACC
> >      gcgid : >db:ID
> >   gcgidacc : >db:ID ACC
> >       dbid : >db ID
> >       ncbi : | formats
> > ID line format [idacc]:
> > Database directory [.]: /var/data/blast_db
> > Wildcard database filename [*.dat]: ecoli
> > Database name: ecoli
> > [marcus at neo blast_db]$ dbifasta
> > Index a fasta database
> >     simple : >ID
> >      idacc : >ID ACC
> >      gcgid : >db:ID
> >   gcgidacc : >db:ID ACC
> >       dbid : >db ID
> >       ncbi : | formats
> > ID line format [idacc]:
> > Database directory [.]: /var/data/blast_db
> > Wildcard database filename [*.dat]: ecoli.nt
> > Database name: ecoli
> > Release number [0.0]:
> > Index date [00/00/00]:
> >
> >
> > Thanks again!
> > Marcus
> >
> >
> > On Tue, 2004-02-17 at 15:50, J?r?me Laroche wrote:
> >> Marcus,
> >>
> >> as suggested earlier by David, take a different name for your 
> >> database.
> >> Take only ecoli or something else. I try this with my data and I got
> >> the same problem.
> >>
> >>
> >> Jerome
> >>
> >> Centre de bioinformatique
> >> Pavillon Charles-Eug?ne-Marchand
> >> Bureau 4233d
> >> t?l: 418-656-2131 poste 6184
> >> fax: 418-656-7176
> >> www.bioinfo.ulaval.ca
> >> Le 04-02-17, ? 10:41, Marcus Claesson a ?crit :
> >>
> >>>
> >>>> 'seqret ecoli.nt:\*' perhaps?
> >>>
> >>> Nope, same bad result...
> >>>
> >>> /M
> >>>
> >>
> >
> 



From gwilliam at hgmp.mrc.ac.uk  Wed Feb 18 08:47:31 2004
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Wed, 18 Feb 2004 13:47:31 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
References: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk>
		 <1077032461.5582.34.camel@morpheus.ucc.ie>
		 <FB53EFC8-6160-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
		 <1077035334.5582.38.camel@morpheus.ucc.ie>
		 <11B65834-6169-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca> <1077111643.25361.59.camel@morpheus.ucc.ie>
Message-ID: <40336CF3.18E39E7C@hgmp.mrc.ac.uk>

Marcus Claesson wrote:
> But this doesn't work and I don't know why since I added the 'des
> field'. Are queries like these suppose to work by the way?
> 
> [marcus]$ seqret ecoli_nt:\*mitochondrio\* -auto -stdout
> Error: Unable to read sequence 'ecoli_nt:*mitochondrio*'
> Died: seqret terminated: Bad value for '-sequence' with -auto defined

The correct syntax should be:
seqret ecoli_nt-des:\*mitochondrio\* -auto -stdout
See:
http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Themes/UniformSequenceAddress.html#keys

-- 
Gary Williams
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494522			Fax: +44 1223 494512
E-mail: gwilliam at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk


From m.claesson at student.ucc.ie  Wed Feb 18 09:52:08 2004
From: m.claesson at student.ucc.ie (Marcus Claesson)
Date: 18 Feb 2004 14:52:08 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <40336D9C.1E5D2AF4@hgmp.mrc.ac.uk>
References: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk>
	 <1077032461.5582.34.camel@morpheus.ucc.ie>
	 <FB53EFC8-6160-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
	 <1077035334.5582.38.camel@morpheus.ucc.ie>
	 <11B65834-6169-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
	 <1077111643.25361.59.camel@morpheus.ucc.ie>
	 <40336CF3.18E39E7C@hgmp.mrc.ac.uk>  <40336D9C.1E5D2AF4@hgmp.mrc.ac.uk>
Message-ID: <1077115928.25361.94.camel@morpheus.ucc.ie>

That works fine now, thanks!

But I continue struggling with upcoming problems and you must be tired
of me asking questions all the time... (It's either me or the emboss man
pages that are bad, probably a mix ;))

Anyway, when I want to create a second database ecoli_aa, dbifasta seems
to overwrite the old indexfiles.

This works all fine:

[marcus]$ dbifasta -idformat ncbi -directory /var/data/blast_db
-filenames ecoli.nt -fields des -dbname ecoli_nt -release 0.0 -date
00/00/00
[marcus]$ seqret ecoli_nt: -auto -stdout|head
>AE000111 AE000111.1 Escherichia coli K-12 MG1655 section 1 of 400 of
the complete genome
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
ACAA

I add a second database: 

[marcus]$ dbifasta -idformat ncbi -directory /var/data/blast_db
-filenames ecoli.aa -fields des -dbname ecoli_aa -release 0.0 -date
00/00/00

And when I seqret the old ecoli_nt I get the new ecoli_aa entries
instead:

[marcus]$ seqret ecoli_nt: -auto -stdout|head
>AAC73112.1 (AE000111) thr operon leader peptide [Escherichia coli]
MKRISTTITTTITITTGNGAG
>AAC73113.1 (AE000111) aspartokinase I, homoserine dehydrogenase I
[Escherichia coli]
MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA
LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA
ALICRGEKMSIAIMAGV


I tried to run dbifasta for both fasta files at the same time but it
didn't work:
dbifasta -idformat ncbi -directory /var/data/blast_db -filenames
ecoli.nt ecoli.aa -fields des -dbname ecoli_nt ecoli_aa -release 0.0
-date 00/00/00

How can new databases be added without overwriting the old indexfiles?


/Marcus




On Wed, 2004-02-18 at 13:50, Gary Williams, Tel 01223 494522 wrote:
> "Gary Williams, Tel 01223 494522" wrote:
> > 
> > Marcus Claesson wrote:
> > > But this doesn't work and I don't know why since I added the 'des
> > > field'. Are queries like these suppose to work by the way?
> > >
> > > [marcus]$ seqret ecoli_nt:\*mitochondrio\* -auto -stdout
> > > Error: Unable to read sequence 'ecoli_nt:*mitochondrio*'
> > > Died: seqret terminated: Bad value for '-sequence' with -auto defined
> > 
> > The correct syntax should be:
> > seqret ecoli_nt-des:\*mitochondrio\* -auto -stdout
> > See:
> > http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Themes/UniformSequenceAddress.html#keys
> 
> I think that the '*' are not required, so:
> seqret ecoli_nt-des:mitochondrio -auto -stdout



From jlaroche at bioinfo.ulaval.ca  Wed Feb 18 10:02:33 2004
From: jlaroche at bioinfo.ulaval.ca (=?ISO-8859-1?Q?J=E9r=F4me_Laroche?=)
Date: Wed, 18 Feb 2004 10:02:33 -0500
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <1077115928.25361.94.camel@morpheus.ucc.ie>
References: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk> <1077032461.5582.34.camel@morpheus.ucc.ie> <FB53EFC8-6160-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca> <1077035334.5582.38.camel@morpheus.ucc.ie> <11B65834-6169-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca> <1077111643.25361.59.camel@morpheus.ucc.ie> <40336CF3.18E39E7C@hgmp.mrc.ac.uk>  <40336D9C.1E5D2AF4@hgmp.mrc.ac.uk> <1077115928.25361.94.camel@morpheus.ucc.ie>
Message-ID: <7AFB6596-6223-11D8-A3F2-000A95CDA6C0@bioinfo.ulaval.ca>

Marcus,

yes, the indexed files will always have the same names (I think this is  
in the EMBOSS administrator's guide):

acnum.hit  acnum.trg  division.lkp  entrynam.idx

That's why you must put these files in different directories. The  
sequence files could be in the same directory.


Jerome

Centre de bioinformatique
Pavillon Charles-Eug?ne-Marchand
Bureau 4233d
t?l: 418-656-2131 poste 6184
fax: 418-656-7176
www.bioinfo.ulaval.ca
Le 04-02-18, ? 09:52, Marcus Claesson a ?crit :

> That works fine now, thanks!
>
> But I continue struggling with upcoming problems and you must be tired
> of me asking questions all the time... (It's either me or the emboss  
> man
> pages that are bad, probably a mix ;))
>
> Anyway, when I want to create a second database ecoli_aa, dbifasta  
> seems
> to overwrite the old indexfiles.
>
> This works all fine:
>
> [marcus]$ dbifasta -idformat ncbi -directory /var/data/blast_db
> -filenames ecoli.nt -fields des -dbname ecoli_nt -release 0.0 -date
> 00/00/00
> [marcus]$ seqret ecoli_nt: -auto -stdout|head
>> AE000111 AE000111.1 Escherichia coli K-12 MG1655 section 1 of 400 of
> the complete genome
> AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
> TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
> TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
> ACAA
>
> I add a second database:
>
> [marcus]$ dbifasta -idformat ncbi -directory /var/data/blast_db
> -filenames ecoli.aa -fields des -dbname ecoli_aa -release 0.0 -date
> 00/00/00
>
> And when I seqret the old ecoli_nt I get the new ecoli_aa entries
> instead:
>
> [marcus]$ seqret ecoli_nt: -auto -stdout|head
>> AAC73112.1 (AE000111) thr operon leader peptide [Escherichia coli]
> MKRISTTITTTITITTGNGAG
>> AAC73113.1 (AE000111) aspartokinase I, homoserine dehydrogenase I
> [Escherichia coli]
> MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA
> LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA
> ALICRGEKMSIAIMAGV
>
>
> I tried to run dbifasta for both fasta files at the same time but it
> didn't work:
> dbifasta -idformat ncbi -directory /var/data/blast_db -filenames
> ecoli.nt ecoli.aa -fields des -dbname ecoli_nt ecoli_aa -release 0.0
> -date 00/00/00
>
> How can new databases be added without overwriting the old indexfiles?
>
>
> /Marcus
>
>
>
>
> On Wed, 2004-02-18 at 13:50, Gary Williams, Tel 01223 494522 wrote:
>> "Gary Williams, Tel 01223 494522" wrote:
>>>
>>> Marcus Claesson wrote:
>>>> But this doesn't work and I don't know why since I added the 'des
>>>> field'. Are queries like these suppose to work by the way?
>>>>
>>>> [marcus]$ seqret ecoli_nt:\*mitochondrio\* -auto -stdout
>>>> Error: Unable to read sequence 'ecoli_nt:*mitochondrio*'
>>>> Died: seqret terminated: Bad value for '-sequence' with -auto  
>>>> defined
>>>
>>> The correct syntax should be:
>>> seqret ecoli_nt-des:\*mitochondrio\* -auto -stdout
>>> See:
>>> http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Themes/ 
>>> UniformSequenceAddress.html#keys
>>
>> I think that the '*' are not required, so:
>> seqret ecoli_nt-des:mitochondrio -auto -stdout
>



From gwilliam at hgmp.mrc.ac.uk  Wed Feb 18 10:04:15 2004
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Wed, 18 Feb 2004 15:04:15 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
References: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk>
		 <1077032461.5582.34.camel@morpheus.ucc.ie>
		 <FB53EFC8-6160-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
		 <1077035334.5582.38.camel@morpheus.ucc.ie>
		 <11B65834-6169-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
		 <1077111643.25361.59.camel@morpheus.ucc.ie>
		 <40336CF3.18E39E7C@hgmp.mrc.ac.uk>  <40336D9C.1E5D2AF4@hgmp.mrc.ac.uk> <1077115928.25361.94.camel@morpheus.ucc.ie>
Message-ID: <40337EEF.88E2CE65@hgmp.mrc.ac.uk>

Marcus Claesson wrote:

> How can new databases be added without overwriting the old indexfiles?

You must have the index files in separate directories because the
indices made by the dbi* programs always have the same names (acnum.hit,
acnum.trg, division.lkb, entryname.idx etc.)

If you have the database files in the same directory, you must put the
index files in other directories (maybe sub-directories?) and specify
the directory name by:
indexdirectory
See:
http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Usa/databases.html#attr
for details

-- 
Gary Williams
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494522			Fax: +44 1223 494512
E-mail: gwilliam at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk


From pmr at ebi.ac.uk  Wed Feb 18 10:07:03 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Wed, 18 Feb 2004 15:07:03 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <1077115928.25361.94.camel@morpheus.ucc.ie>
References: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk>	 <1077032461.5582.34.camel@morpheus.ucc.ie>	 <FB53EFC8-6160-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>	 <1077035334.5582.38.camel@morpheus.ucc.ie>	 <11B65834-6169-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>	 <1077111643.25361.59.camel@morpheus.ucc.ie>	 <40336CF3.18E39E7C@hgmp.mrc.ac.uk>  <40336D9C.1E5D2AF4@hgmp.mrc.ac.uk> <1077115928.25361.94.camel@morpheus.ucc.ie>
Message-ID: <40337F97.8080405@ebi.ac.uk>

Marcus Claesson wrote:

> But I continue struggling with upcoming problems and you must be tired
> of me asking questions all the time... (It's either me or the emboss man
> pages that are bad, probably a mix ;))
> 
> Anyway, when I want to create a second database ecoli_aa, dbifasta seems
> to overwrite the old indexfiles.

The index files always have the same name.

But you can put the index files in a new directory with the 
-indexdirectory option of dbifasta

The index directory goes into your database definition as

indexdirectory: "/full/path/toindex/files/"

Hope this helps

Peter Rice



From aml at computerfulfillment.com  Wed Feb 18 12:59:50 2004
From: aml at computerfulfillment.com (American Laboratory)
Date: Wed, 18 Feb 2004 12:59:50 -0500
Subject: [EMBOSS] A professional journal for you.
Message-ID: <03344902.20040218125950@computerfulfillment.com>






To Subscribe
Go To:
http://www.icainfo.com/aml/appintro.asp?acct=&amp;Renew=YES&amp;Priority=RW1003&amp;lastfour=

Following are the themes to be featured in AL: 
November Microscopy, Optics, and Image Analysis 
December Pharmaceutical Analysis, Molecular Spectroscopy, EAS 
January Annual ISC Buyers' Guide,Thermal Analysis, Gas Chromatography 
February Pittcon 2004 New Analytical Instrumentation for Separation Science and Spectroscopy 
March Advances in Laboratory Software and Data Management 
April Microchemical Analysis, Sample Preparation 




Dear Emboss, 

Please accept my invitation to continue to receive a free subscription to our journal, American Laboratory.

American Laboratory covers the disciplines of analytical and bioanalytical chemistry, drug discovery, laboratory software and informatics. Each issue features articles from leading scientists from around the world reviewing applications of instrumentation and new measurement technology.

To continue your FREE subscription to American Laboratory, please click on the following link. 

http://www.icainfo.com/aml/appintro.asp?acct=&amp;Renew=YES&amp;Priority=RW1003&amp;lastfour=


I am confident that you will enjoy our journal and find it to be of significant professional value.

I look forward to hearing from you.

Sincerely yours,

Brian Howard, Ph.D.
Editor





















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From: R-1-721447-22941564-2-8269-US2-D7857328 at xmr3.com (International Scientific Communications, Inc.)
Date: Thu, 19 Feb 2004 00:32:37 -0500
Subject: [EMBOSS] Laboratory Instrumentation News - February 2004
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From: block at xmr3.com (Customer Service)
Date: 19 Feb 2004 20:13:20 -0000
Subject: [EMBOSS] Removal Notification
Message-ID: <20040219201320.13598.qmail@xmr3.com>

By the end of the day, the address:
      emboss at embnet.org
will no longer receive email sent from:
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If you believe that this change was made in error,
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From pmr at ebi.ac.uk  Fri Feb 20 08:13:50 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 20 Feb 2004 13:13:50 +0000
Subject: [EMBOSS] Coderet
In-Reply-To: <OF7B32F5D8.E402B94A-ONCA256E28.000458A8@nre.vic.gov.au>
References: <OF7B32F5D8.E402B94A-ONCA256E28.000458A8@nre.vic.gov.au>
Message-ID: <4036080E.2040403@ebi.ac.uk>

Hi Sean

Sean.Maceachern at dpi.vic.gov.au wrote:

> I have not done any programming in c++ so I was hoping that someone
> might be able how to suggest how I can get the output from coderet to
> resemble that of NCBI's
> 
> I think it could be done by parsing the sections in BOLD from the first few lines of the feature table.
> 
> LOCUS       NM_000367               2742 bp    mRNA    linear   PRI
> 31-OCT-2000
> DEFINITION  Homo sapiens thiopurine S-methyltransferase (TPMT), mRNA.
> ACCESSION   NM_000367
> VERSION     NM_000367.1  GI:4507652
> KEYWORDS    .
> SOURCE      Homo sapiens (human)
> 
> 
> ie)
> 
> 
>>gi|4507652 Homo sapiens thiopurine S-methyltransferase (TPMT), mRNA
> 
> ATGGATGGTACAAGAACTTCACTTGACATTGAAGAGTACTCGGATACTGAGGTACAGAAA
> AACCAAGTACTAACTCTGGAAGAATGGCAAGACAAGTGGGTGAACGGCAAGACTGCTTTT
> 
> 
> Does anyone know if this already exists in a coderet option or how I would
> be able to modfiy this in the original script?

Possible .... it would be nice to have a description in the output, but 
we have to be careful where we take it from.

This is a simple REFSEQ entry with only one CDS, but coderet has to also 
work on large bacterial genome contigs.

This means we can only get the taxonomy from the top of the entry.

However, this CDS does have information in the (true) feature table:

CDS             66..803
                 /gene="TPMT"
                 /EC_number="2.1.1.67"
                 /codon_start=1
                 /product="thiopurine S-methyltransferase"
                 /protein_id="NP_000358.1"
                 /db_xref="GI:4507653"
                 /db_xref="LocusID:7172"
                 /db_xref="MIM:187680"
                 /translation="MDGTRTSL...LYLLTEK"

So, for the description line you wanted:

 >gi|4507652 Homo sapiens thiopurine S-methyltransferase (TPMT), mRNA

We can get:

"Homo" sapiens from the SOURCE line (EMBOSS already parses this)

"TPMT" from the /gene qualifier (if present)

"thiopurine S-methyltransferase" from the /product qualifier (if present)

we can also ... if other qualifiers are missing, try /note= or simply 
use the entry description and some CDS counter:
"CDS 1 from Homo sapiens thiopurine S-methyltransferase (TPMT), mRNA."

The mRNA at the end is tricky ... I would much prefer to use the feature 
type (CDS) because that is what we have.

So you would have a description (in FASTA or NCBI or any other format) of:

 >NM_000367 Homo sapiens thiopurine S-methyltransferase (TPMT), CDS

regards,

Peter Rice



From abl at computerfulfillment.com  Fri Feb 20 10:22:36 2004
From: abl at computerfulfillment.com (American Biotechnology Laboratory)
Date: Fri, 20 Feb 2004 10:22:36 -0500
Subject: [EMBOSS] A professional journal for you.
Message-ID: <65636188.20040220102236@computerfulfillment.com>






To Subscribe
Go To:
http://www.icainfo.com/aml/appintro.asp?Priority=SARAB


Following are the themes to be featured in AL: 
November Microscopy, Optics, and Image Analysis 
December Pharmaceutical Analysis, Molecular Spectroscopy, EAS 
January Annual ISC Buyers' Guide,Thermal Analysis, Gas Chromatography 
February Pittcon 2004 New Analytical Instrumentation for Separation Science and Spectroscopy 
March Advances in Laboratory Software and Data Management 
April Microchemical Analysis, Sample Preparation 




Dear Colleague, 

Please accept my invitation to receive a free subscription to our journal, American Laboratory.

American Laboratory covers the disciplines of analytical and bioanalytical chemistry, drug discovery, laboratory software and informatics. Each issue features articles from leading scientists from around the world reviewing applications of instrumentation and new measurement technology.

For your FREE subscription to American Laboratory, please click on the following link. 

http://www.icainfo.com/aml/appintro.asp?Priority=PEPAB3


I am confident that you will enjoy our journal and find it to be of significant professional value.

I look forward to hearing from you.

Sincerely yours,

Brian Howard, Ph.D.
Editor

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From pmr at ebi.ac.uk  Mon Feb 23 05:22:37 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Mon, 23 Feb 2004 10:22:37 +0000
Subject: [EMBOSS] Staden and EMBOSS 2.8.O
In-Reply-To: <2DC41140A89ED411989D00508BDCD9ED01E28CD0@bi-exsrv1.iapc.bbsrc.ac.uk>
References: <2DC41140A89ED411989D00508BDCD9ED01E28CD0@bi-exsrv1.iapc.bbsrc.ac.uk>
Message-ID: <4039D46D.6000305@ebi.ac.uk>

simon andrews (BI) wrote:

> 
>>-----Original Message-----
>>From: Guy Bottu [mailto:gbottu at ben.vub.ac.be] 
>>Subject: [EMBOSS] Staden and EMBOSS 2.8.O
>>
>>Unfortunately there is no support for Staden anymore (well, 
>>it was recently announced that James Bonfield is working 
>>at Sanger Centre, but according to the Web page he is 
>>only developing gap4, not spin). Does someone know more about it ?
> 
> 
> James recently announced that the MRC have finally agreed to release Staden under an opensource licence.  It is therefore now being hosted and developed as a sourceforge project:
> 
> http://staden.sourceforge.net/
> 
> https://sourceforge.net/projects/staden
> 
> ..therefore if you're up to making the changes yourself you can submit patches to the project, or if not you can file it as a bug which someone else will hopefully pick up.

I have updated EMBSOS in the past to produce graphics in SPIN for some 
proggrams that did not do it "normally".

I recently volunteered to update SPIN for EMBOSS 2.8.1 (due out soon) 
and will put the updates on the Staden SourceForge site and into the 
EMBOSS distribution.

James Bonfield is here on campus so we can easily coordinate this. I may 
have a volunteer to test the SPIN/EMBOSS interface - but more would be 
welcome!

regards,

Peter Rice



From mad at biol.unlp.edu.ar  Mon Feb 23 09:52:52 2004
From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=)
Date: Mon, 23 Feb 2004 11:52:52 -0300
Subject: [EMBOSS] cannot compile a single program
Message-ID: <403A13C4.4020407@biol.unlp.edu.ar>

Dear list,

I'm trying to add a program to our EMBOSS-2.6.0 installation.
These are the steps I followed:
- added clustal.c into EMBOSS_distro/emboss dir and clustal.acd under 
EMBOSS_distro/emboss/acd
- then edited EMBOSS_distro/emboss/Makefile.am and added 'clustal' to the 
'bin_PROGRAMS' section and the line 'clustal_SOURCES = clustal.c' to the same 
Makefile.am
- when doing a 'make clustal' into EMBOSS_distro/emboss dir I get this

> # make clustal
> cd .. && /bin/sh ./config.status emboss/Makefile depfiles
> config.status: creating emboss/Makefile
> config.status: executing depfiles commands
> Makefile:2179: aaindexextract.Po: No such file or directory
> Makefile:2180: abiview.Po: No such file or directory
> Makefile:2181: acdc.Po: No such file or directory
> Makefile:2182: ajtest.Po: No such file or directory
> Makefile:2183: antigenic.Po: No such file or directory
> Makefile:2184: backtranseq.Po: No such file or directory
> Makefile:2185: banana.Po: No such file or directory
> Makefile:2186: biosed.Po: No such file or directory
> Makefile:2187: btwisted.Po: No such file or directory
> Makefile:2188: cai.Po: No such file or directory
> Makefile:2189: chaos.Po: No such file or directory
> Makefile:2190: charge.Po: No such file or directory
> Makefile:2191: checktrans.Po: No such file or directory
> Makefile:2192: chips.Po: No such file or directory
> Makefile:2193: cirdna.Po: No such file or directory
> Makefile:2194: clustal.Po: No such file or directory
> Makefile:2195: codcmp.Po: No such file or directory
> Makefile:2196: coderet.Po: No such file or directory
> Makefile:2197: complex.Po: No such file or directory
> Makefile:2198: compseq.Po: No such file or directory
> Makefile:2199: cons.Po: No such file or directory
> Makefile:2200: corbatest.Po: No such file or directory
> Makefile:2201: cpgplot.Po: No such file or directory
> Makefile:2202: cpgreport.Po: No such file or directory
> Makefile:2203: cusp.Po: No such file or directory
> Makefile:2204: cutgextract.Po: No such file or directory
> Makefile:2205: cutseq.Po: No such file or directory
> Makefile:2206: dan.Po: No such file or directory
> Makefile:2207: dbiblast.Po: No such file or directory
> Makefile:2208: dbifasta.Po: No such file or directory
> Makefile:2209: dbiflat.Po: No such file or directory
> Makefile:2210: dbigcg.Po: No such file or directory
> Makefile:2211: degapseq.Po: No such file or directory
> Makefile:2212: demoalign.Po: No such file or directory
> Makefile:2213: demofeatures.Po: No such file or directory
> Makefile:2214: demolist.Po: No such file or directory
> Makefile:2215: demoreport.Po: No such file or directory
> Makefile:2216: demosequence.Po: No such file or directory
> Makefile:2217: demostring.Po: No such file or directory
> Makefile:2218: demotable.Po: No such file or directory
> Makefile:2219: descseq.Po: No such file or directory
> Makefile:2220: diffseq.Po: No such file or directory
> Makefile:2221: digest.Po: No such file or directory
> Makefile:2222: distmat.Po: No such file or directory
> Makefile:2223: dotmatcher.Po: No such file or directory
> Makefile:2224: dotpath.Po: No such file or directory
> Makefile:2225: dottup.Po: No such file or directory
> Makefile:2226: dreg.Po: No such file or directory
> Makefile:2227: einverted.Po: No such file or directory
> Makefile:2228: embossdata.Po: No such file or directory
> Makefile:2229: embossversion.Po: No such file or directory
> Makefile:2230: emma.Po: No such file or directory
> Makefile:2231: emowse.Po: No such file or directory
> Makefile:2232: entrails.Po: No such file or directory
> Makefile:2233: entret.Po: No such file or directory
> Makefile:2234: eprimer3.Po: No such file or directory
> Makefile:2235: equicktandem.Po: No such file or directory
> Makefile:2236: est2genome.Po: No such file or directory
> Makefile:2237: etandem.Po: No such file or directory
> Makefile:2238: extractfeat.Po: No such file or directory
> Makefile:2239: extractseq.Po: No such file or directory
> Makefile:2240: findkm.Po: No such file or directory
> Makefile:2241: freak.Po: No such file or directory
> Makefile:2242: fuzznuc.Po: No such file or directory
> Makefile:2243: fuzzpro.Po: No such file or directory
> Makefile:2244: fuzztran.Po: No such file or directory
> Makefile:2245: garnier.Po: No such file or directory
> Makefile:2246: geecee.Po: No such file or directory
> Makefile:2247: getorf.Po: No such file or directory
> Makefile:2248: helixturnhelix.Po: No such file or directory
> Makefile:2249: histogramtest.Po: No such file or directory
> Makefile:2250: hmoment.Po: No such file or directory
> Makefile:2251: iep.Po: No such file or directory
> Makefile:2252: infoalign.Po: No such file or directory
> Makefile:2253: infoseq.Po: No such file or directory
> Makefile:2254: intconv.Po: No such file or directory
> Makefile:2255: isochore.Po: No such file or directory
> Makefile:2256: jembossctl.Po: No such file or directory
> Makefile:2257: lindna.Po: No such file or directory
> Makefile:2258: listor.Po: No such file or directory
> Makefile:2259: marscan.Po: No such file or directory
> Makefile:2260: maskfeat.Po: No such file or directory
> Makefile:2261: maskseq.Po: No such file or directory
> Makefile:2262: matcher.Po: No such file or directory
> Makefile:2263: megamerger.Po: No such file or directory
> Makefile:2264: merger.Po: No such file or directory
> Makefile:2265: msbar.Po: No such file or directory
> Makefile:2266: mwcontam.Po: No such file or directory
> Makefile:2267: mwfilter.Po: No such file or directory
> Makefile:2268: needle.Po: No such file or directory
> Makefile:2269: newcpgreport.Po: No such file or directory
> Makefile:2270: newcpgseek.Po: No such file or directory
> Makefile:2271: newseq.Po: No such file or directory
> Makefile:2272: noreturn.Po: No such file or directory
> Makefile:2273: notseq.Po: No such file or directory
> Makefile:2274: nthseq.Po: No such file or directory
> Makefile:2275: octanol.Po: No such file or directory
> Makefile:2276: oddcomp.Po: No such file or directory
> Makefile:2277: palindrome.Po: No such file or directory
> Makefile:2278: pasteseq.Po: No such file or directory
> Makefile:2279: patmatdb.Po: No such file or directory
> Makefile:2280: patmatmotifs.Po: No such file or directory
> Makefile:2281: patmattest.Po: No such file or directory
> Makefile:2282: pepcoil.Po: No such file or directory
> Makefile:2283: pepinfo.Po: No such file or directory
> Makefile:2284: pepnet.Po: No such file or directory
> Makefile:2285: pepstats.Po: No such file or directory
> Makefile:2286: pepwheel.Po: No such file or directory
> Makefile:2287: pepwindow.Po: No such file or directory
> Makefile:2288: pepwindowall.Po: No such file or directory
> Makefile:2289: pestfind.Po: No such file or directory
> Makefile:2290: plotcon.Po: No such file or directory
> Makefile:2291: plotorf.Po: No such file or directory
> Makefile:2292: polydot.Po: No such file or directory
> Makefile:2293: preg.Po: No such file or directory
> Makefile:2294: prettyplot.Po: No such file or directory
> Makefile:2295: prettyseq.Po: No such file or directory
> Makefile:2296: prima.Po: No such file or directory
> Makefile:2297: primers.Po: No such file or directory
> Makefile:2298: primersearch.Po: No such file or directory
> Makefile:2299: printsextract.Po: No such file or directory
> Makefile:2300: profit.Po: No such file or directory
> Makefile:2301: prophecy.Po: No such file or directory
> Makefile:2302: prophet.Po: No such file or directory
> Makefile:2303: prosextract.Po: No such file or directory
> Makefile:2304: pscan.Po: No such file or directory
> Makefile:2305: rebaseextract.Po: No such file or directory
> Makefile:2306: recoder.Po: No such file or directory
> Makefile:2307: redata.Po: No such file or directory
> Makefile:2308: remap.Po: No such file or directory
> Makefile:2309: restover.Po: No such file or directory
> Makefile:2310: restrict.Po: No such file or directory
> Makefile:2311: revseq.Po: No such file or directory
> Makefile:2312: seealso.Po: No such file or directory
> Makefile:2313: seqinfo.Po: No such file or directory
> Makefile:2314: seqmatchall.Po: No such file or directory
> Makefile:2315: seqret.Po: No such file or directory
> Makefile:2316: seqretall.Po: No such file or directory
> Makefile:2317: seqretallfeat.Po: No such file or directory
> Makefile:2318: seqretset.Po: No such file or directory
> Makefile:2319: seqretsingle.Po: No such file or directory
> Makefile:2320: seqretsplit.Po: No such file or directory
> Makefile:2321: showalign.Po: No such file or directory
> Makefile:2322: showdb.Po: No such file or directory
> Makefile:2323: showfeat.Po: No such file or directory
> Makefile:2324: showorf.Po: No such file or directory
> Makefile:2325: showseq.Po: No such file or directory
> Makefile:2326: shuffleseq.Po: No such file or directory
> Makefile:2327: sigcleave.Po: No such file or directory
> Makefile:2328: silent.Po: No such file or directory
> Makefile:2329: sirna.Po: No such file or directory
> Makefile:2330: sixpack.Po: No such file or directory
> Makefile:2331: skipseq.Po: No such file or directory
> Makefile:2332: splitter.Po: No such file or directory
> Makefile:2333: stretcher.Po: No such file or directory
> Makefile:2334: stssearch.Po: No such file or directory
> Makefile:2335: supermatcher.Po: No such file or directory
> Makefile:2336: syco.Po: No such file or directory
> Makefile:2337: testplot.Po: No such file or directory
> Makefile:2338: textsearch.Po: No such file or directory
> Makefile:2339: tfextract.Po: No such file or directory
> Makefile:2340: tfm.Po: No such file or directory
> Makefile:2341: tfscan.Po: No such file or directory
> Makefile:2342: tmap.Po: No such file or directory
> Makefile:2343: tranalign.Po: No such file or directory
> Makefile:2344: transeq.Po: No such file or directory
> Makefile:2345: treetypedisplay.Po: No such file or directory
> Makefile:2346: trimest.Po: No such file or directory
> Makefile:2347: trimseq.Po: No such file or directory
> Makefile:2348: twofeat.Po: No such file or directory
> Makefile:2349: union.Po: No such file or directory
> Makefile:2350: vectorstrip.Po: No such file or directory
> Makefile:2351: water.Po: No such file or directory
> Makefile:2352: whichdb.Po: No such file or directory
> Makefile:2353: wobble.Po: No such file or directory
> Makefile:2354: wordcount.Po: No such file or directory
> Makefile:2355: wordmatch.Po: No such file or directory
> Makefile:2356: wossname.Po: No such file or directory
> Makefile:2357: yank.Po: No such file or directory
> make: *** No rule to make target `yank.Po'.  Stop.
> #

What am I missing?

Regards,

martin

-- 
Mart?n Sarachu
mad at biol.unlp.edu.ar
EMBNet Argentina
http://www.ar.embnet.org


From d.gatherer at vir.gla.ac.uk  Mon Feb 23 10:06:11 2004
From: d.gatherer at vir.gla.ac.uk (Derek Gatherer)
Date: Mon, 23 Feb 2004 15:06:11 +0000
Subject: [EMBOSS] cannot compile a single program
In-Reply-To: <403A13C4.4020407@biol.unlp.edu.ar>
Message-ID: <5.2.1.1.1.20040223145844.00acecd0@udcf.gla.ac.uk>

Hi

You need to be working from the cvs version of emboss:

 >cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss login
 >cvs
 >cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss checkout emboss
 >cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss logout

Assuming you have got this, you need to do what you did, ie. add the code 
in the correct place and modify the makefile appropriately, and then go to 
the correct directory and enter:

 >aclocal -I m4
 >autoconf -v
 >automake -a
 >./configure
 >make
 >make check
 >make install
 >make clean

You'll need up to date versions of autoconf and automake.  We add lots of 
local code - it's convoluted to do all this, but it always works.

Cheers
Derek

At 11:52 23/02/2004 -0300, you wrote:
>Dear list,
>
>I'm trying to add a program to our EMBOSS-2.6.0 installation.
>These are the steps I followed:
>- added clustal.c into EMBOSS_distro/emboss dir and clustal.acd under 
>EMBOSS_distro/emboss/acd
>- then edited EMBOSS_distro/emboss/Makefile.am and added 'clustal' to the 
>'bin_PROGRAMS' section and the line 'clustal_SOURCES = clustal.c' to the 
>same Makefile.am
>- when doing a 'make clustal' into EMBOSS_distro/emboss dir I get this
>
>># make clustal
>>cd .. && /bin/sh ./config.status emboss/Makefile depfiles
>>config.status: creating emboss/Makefile
>>config.status: executing depfiles commands
>>Makefile:2179: aaindexextract.Po: No such file or directory
>>Makefile:2180: abiview.Po: No such file or directory
>>Makefile:2181: acdc.Po: No such file or directory
>>Makefile:2182: ajtest.Po: No such file or directory
>>Makefile:2183: antigenic.Po: No such file or directory
>>Makefile:2184: backtranseq.Po: No such file or directory
>>Makefile:2185: banana.Po: No such file or directory
>>Makefile:2186: biosed.Po: No such file or directory
>>Makefile:2187: btwisted.Po: No such file or directory
>>Makefile:2188: cai.Po: No such file or directory
>>Makefile:2189: chaos.Po: No such file or directory
>>Makefile:2190: charge.Po: No such file or directory
>>Makefile:2191: checktrans.Po: No such file or directory
>>Makefile:2192: chips.Po: No such file or directory
>>Makefile:2193: cirdna.Po: No such file or directory
>>Makefile:2194: clustal.Po: No such file or directory
>>Makefile:2195: codcmp.Po: No such file or directory
>>Makefile:2196: coderet.Po: No such file or directory
>>Makefile:2197: complex.Po: No such file or directory
>>Makefile:2198: compseq.Po: No such file or directory
>>Makefile:2199: cons.Po: No such file or directory
>>Makefile:2200: corbatest.Po: No such file or directory
>>Makefile:2201: cpgplot.Po: No such file or directory
>>Makefile:2202: cpgreport.Po: No such file or directory
>>Makefile:2203: cusp.Po: No such file or directory
>>Makefile:2204: cutgextract.Po: No such file or directory
>>Makefile:2205: cutseq.Po: No such file or directory
>>Makefile:2206: dan.Po: No such file or directory
>>Makefile:2207: dbiblast.Po: No such file or directory
>>Makefile:2208: dbifasta.Po: No such file or directory
>>Makefile:2209: dbiflat.Po: No such file or directory
>>Makefile:2210: dbigcg.Po: No such file or directory
>>Makefile:2211: degapseq.Po: No such file or directory
>>Makefile:2212: demoalign.Po: No such file or directory
>>Makefile:2213: demofeatures.Po: No such file or directory
>>Makefile:2214: demolist.Po: No such file or directory
>>Makefile:2215: demoreport.Po: No such file or directory
>>Makefile:2216: demosequence.Po: No such file or directory
>>Makefile:2217: demostring.Po: No such file or directory
>>Makefile:2218: demotable.Po: No such file or directory
>>Makefile:2219: descseq.Po: No such file or directory
>>Makefile:2220: diffseq.Po: No such file or directory
>>Makefile:2221: digest.Po: No such file or directory
>>Makefile:2222: distmat.Po: No such file or directory
>>Makefile:2223: dotmatcher.Po: No such file or directory
>>Makefile:2224: dotpath.Po: No such file or directory
>>Makefile:2225: dottup.Po: No such file or directory
>>Makefile:2226: dreg.Po: No such file or directory
>>Makefile:2227: einverted.Po: No such file or directory
>>Makefile:2228: embossdata.Po: No such file or directory
>>Makefile:2229: embossversion.Po: No such file or directory
>>Makefile:2230: emma.Po: No such file or directory
>>Makefile:2231: emowse.Po: No such file or directory
>>Makefile:2232: entrails.Po: No such file or directory
>>Makefile:2233: entret.Po: No such file or directory
>>Makefile:2234: eprimer3.Po: No such file or directory
>>Makefile:2235: equicktandem.Po: No such file or directory
>>Makefile:2236: est2genome.Po: No such file or directory
>>Makefile:2237: etandem.Po: No such file or directory
>>Makefile:2238: extractfeat.Po: No such file or directory
>>Makefile:2239: extractseq.Po: No such file or directory
>>Makefile:2240: findkm.Po: No such file or directory
>>Makefile:2241: freak.Po: No such file or directory
>>Makefile:2242: fuzznuc.Po: No such file or directory
>>Makefile:2243: fuzzpro.Po: No such file or directory
>>Makefile:2244: fuzztran.Po: No such file or directory
>>Makefile:2245: garnier.Po: No such file or directory
>>Makefile:2246: geecee.Po: No such file or directory
>>Makefile:2247: getorf.Po: No such file or directory
>>Makefile:2248: helixturnhelix.Po: No such file or directory
>>Makefile:2249: histogramtest.Po: No such file or directory
>>Makefile:2250: hmoment.Po: No such file or directory
>>Makefile:2251: iep.Po: No such file or directory
>>Makefile:2252: infoalign.Po: No such file or directory
>>Makefile:2253: infoseq.Po: No such file or directory
>>Makefile:2254: intconv.Po: No such file or directory
>>Makefile:2255: isochore.Po: No such file or directory
>>Makefile:2256: jembossctl.Po: No such file or directory
>>Makefile:2257: lindna.Po: No such file or directory
>>Makefile:2258: listor.Po: No such file or directory
>>Makefile:2259: marscan.Po: No such file or directory
>>Makefile:2260: maskfeat.Po: No such file or directory
>>Makefile:2261: maskseq.Po: No such file or directory
>>Makefile:2262: matcher.Po: No such file or directory
>>Makefile:2263: megamerger.Po: No such file or directory
>>Makefile:2264: merger.Po: No such file or directory
>>Makefile:2265: msbar.Po: No such file or directory
>>Makefile:2266: mwcontam.Po: No such file or directory
>>Makefile:2267: mwfilter.Po: No such file or directory
>>Makefile:2268: needle.Po: No such file or directory
>>Makefile:2269: newcpgreport.Po: No such file or directory
>>Makefile:2270: newcpgseek.Po: No such file or directory
>>Makefile:2271: newseq.Po: No such file or directory
>>Makefile:2272: noreturn.Po: No such file or directory
>>Makefile:2273: notseq.Po: No such file or directory
>>Makefile:2274: nthseq.Po: No such file or directory
>>Makefile:2275: octanol.Po: No such file or directory
>>Makefile:2276: oddcomp.Po: No such file or directory
>>Makefile:2277: palindrome.Po: No such file or directory
>>Makefile:2278: pasteseq.Po: No such file or directory
>>Makefile:2279: patmatdb.Po: No such file or directory
>>Makefile:2280: patmatmotifs.Po: No such file or directory
>>Makefile:2281: patmattest.Po: No such file or directory
>>Makefile:2282: pepcoil.Po: No such file or directory
>>Makefile:2283: pepinfo.Po: No such file or directory
>>Makefile:2284: pepnet.Po: No such file or directory
>>Makefile:2285: pepstats.Po: No such file or directory
>>Makefile:2286: pepwheel.Po: No such file or directory
>>Makefile:2287: pepwindow.Po: No such file or directory
>>Makefile:2288: pepwindowall.Po: No such file or directory
>>Makefile:2289: pestfind.Po: No such file or directory
>>Makefile:2290: plotcon.Po: No such file or directory
>>Makefile:2291: plotorf.Po: No such file or directory
>>Makefile:2292: polydot.Po: No such file or directory
>>Makefile:2293: preg.Po: No such file or directory
>>Makefile:2294: prettyplot.Po: No such file or directory
>>Makefile:2295: prettyseq.Po: No such file or directory
>>Makefile:2296: prima.Po: No such file or directory
>>Makefile:2297: primers.Po: No such file or directory
>>Makefile:2298: primersearch.Po: No such file or directory
>>Makefile:2299: printsextract.Po: No such file or directory
>>Makefile:2300: profit.Po: No such file or directory
>>Makefile:2301: prophecy.Po: No such file or directory
>>Makefile:2302: prophet.Po: No such file or directory
>>Makefile:2303: prosextract.Po: No such file or directory
>>Makefile:2304: pscan.Po: No such file or directory
>>Makefile:2305: rebaseextract.Po: No such file or directory
>>Makefile:2306: recoder.Po: No such file or directory
>>Makefile:2307: redata.Po: No such file or directory
>>Makefile:2308: remap.Po: No such file or directory
>>Makefile:2309: restover.Po: No such file or directory
>>Makefile:2310: restrict.Po: No such file or directory
>>Makefile:2311: revseq.Po: No such file or directory
>>Makefile:2312: seealso.Po: No such file or directory
>>Makefile:2313: seqinfo.Po: No such file or directory
>>Makefile:2314: seqmatchall.Po: No such file or directory
>>Makefile:2315: seqret.Po: No such file or directory
>>Makefile:2316: seqretall.Po: No such file or directory
>>Makefile:2317: seqretallfeat.Po: No such file or directory
>>Makefile:2318: seqretset.Po: No such file or directory
>>Makefile:2319: seqretsingle.Po: No such file or directory
>>Makefile:2320: seqretsplit.Po: No such file or directory
>>Makefile:2321: showalign.Po: No such file or directory
>>Makefile:2322: showdb.Po: No such file or directory
>>Makefile:2323: showfeat.Po: No such file or directory
>>Makefile:2324: showorf.Po: No such file or directory
>>Makefile:2325: showseq.Po: No such file or directory
>>Makefile:2326: shuffleseq.Po: No such file or directory
>>Makefile:2327: sigcleave.Po: No such file or directory
>>Makefile:2328: silent.Po: No such file or directory
>>Makefile:2329: sirna.Po: No such file or directory
>>Makefile:2330: sixpack.Po: No such file or directory
>>Makefile:2331: skipseq.Po: No such file or directory
>>Makefile:2332: splitter.Po: No such file or directory
>>Makefile:2333: stretcher.Po: No such file or directory
>>Makefile:2334: stssearch.Po: No such file or directory
>>Makefile:2335: supermatcher.Po: No such file or directory
>>Makefile:2336: syco.Po: No such file or directory
>>Makefile:2337: testplot.Po: No such file or directory
>>Makefile:2338: textsearch.Po: No such file or directory
>>Makefile:2339: tfextract.Po: No such file or directory
>>Makefile:2340: tfm.Po: No such file or directory
>>Makefile:2341: tfscan.Po: No such file or directory
>>Makefile:2342: tmap.Po: No such file or directory
>>Makefile:2343: tranalign.Po: No such file or directory
>>Makefile:2344: transeq.Po: No such file or directory
>>Makefile:2345: treetypedisplay.Po: No such file or directory
>>Makefile:2346: trimest.Po: No such file or directory
>>Makefile:2347: trimseq.Po: No such file or directory
>>Makefile:2348: twofeat.Po: No such file or directory
>>Makefile:2349: union.Po: No such file or directory
>>Makefile:2350: vectorstrip.Po: No such file or directory
>>Makefile:2351: water.Po: No such file or directory
>>Makefile:2352: whichdb.Po: No such file or directory
>>Makefile:2353: wobble.Po: No such file or directory
>>Makefile:2354: wordcount.Po: No such file or directory
>>Makefile:2355: wordmatch.Po: No such file or directory
>>Makefile:2356: wossname.Po: No such file or directory
>>Makefile:2357: yank.Po: No such file or directory
>>make: *** No rule to make target `yank.Po'.  Stop.
>>#
>
>What am I missing?
>
>Regards,
>
>martin
>
>--
>Mart?n Sarachu
>mad at biol.unlp.edu.ar
>EMBNet Argentina
>http://www.ar.embnet.org



From mad at biol.unlp.edu.ar  Tue Feb 24 08:27:06 2004
From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=)
Date: Tue, 24 Feb 2004 10:27:06 -0300
Subject: [EMBOSS] Cannot configure, auto* tools problem?
Message-ID: <403B512A.10003@biol.unlp.edu.ar>

Dear list,

when running 'configure' I'm getting some errors...

> # ./configure --prefix=/usr/local/emboss
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
> checking build system type... i686-pc-linux-gnu
> checking host system type... i686-pc-linux-gnu
> checking for style of include used by make... GNU
> checking for gcc... gcc
> checking for C compiler default output... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking dependency style of gcc... gcc3
> checking for ld used by GCC... /usr/bin/ld
> checking if the linker (/usr/bin/ld) is GNU ld... yes
> checking for /usr/bin/ld option to reload object files... -r
> checking for BSD-compatible nm... /usr/bin/nm -B
> checking whether ln -s works... yes
> checking how to recognise dependant libraries... pass_all
> checking command to parse /usr/bin/nm -B output... ok
> checking how to run the C preprocessor... gcc -E
> checking for egrep... grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking dlfcn.h usability... yes
> checking dlfcn.h presence... yes
> checking for dlfcn.h... yes
> checking for ranlib... ranlib
> checking for strip... strip
> checking for objdir... .libs
> checking for gcc option to produce PIC... -fPIC
> checking if gcc PIC flag -fPIC works... yes
> checking if gcc static flag -static works... yes
> checking if gcc supports -c -o file.o... yes
> checking if gcc supports -c -o file.lo... yes
> checking if gcc supports -fno-rtti -fno-exceptions... yes
> checking whether the linker (/usr/bin/ld) supports shared libraries... yes
> checking how to hardcode library paths into programs... immediate
> checking whether stripping libraries is possible... yes
> checking dynamic linker characteristics... GNU/Linux ld.so
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... yes
> checking whether to build static libraries... yes
> checking whether -lc should be explicitly linked in... no
> creating libtool
> checking for gawk... (cached) gawk
> checking for gcc... (cached) gcc
> checking whether we are using the GNU C compiler... (cached) yes
> checking whether gcc accepts -g... (cached) yes
> checking for gcc option to accept ANSI C... (cached) none needed
> checking dependency style of gcc... (cached) gcc3
> checking how to run the C preprocessor... gcc -E
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether ln -s works... yes
> checking whether make sets $(MAKE)... (cached) yes
> checking for ranlib... (cached) ranlib
> checking for X... libraries /usr/X11R6/lib, headers /usr/X11R6/include
> checking for gethostbyname... yes
> checking for connect... yes
> checking for remove... yes
> checking for shmat... yes
> checking for IceConnectionNumber in -lICE... yes
> checking for dirent.h that defines DIR... yes
> checking for library containing opendir... none required
> checking for ANSI C header files... (cached) yes
> checking for unistd.h... (cached) yes
> checking for an ANSI C-conforming const... yes
> checking for pid_t... yes
> checking for size_t... yes
> checking whether struct tm is in sys/time.h or time.h... time.h
> checking whether getpgrp requires zero arguments... yes
> checking for strftime... yes
> checking for unistd.h... (cached) yes
> checking vfork.h usability... no
> checking vfork.h presence... no
> checking for vfork.h... no
> checking for fork... yes
> checking for vfork... yes
> checking for working fork... yes
> checking for working vfork... (cached) yes
> checking for vprintf... yes
> checking for _doprnt... no
> checking for memmove... yes
> ./configure: LF_EMBOSS_PATH_XLIB: command not found  << HERE
> checking for gethostbyname in -lc... yes
> checking for socket in -lc... yes
> checking for main in -lm... yes
> ./configure: CHECK_PNGDRIVER: command not found  << HERE
> ./configure: CHECK_JAVA: command not found  << HERE
> ./configure: CHECK_JAVAOS: command not found  << HERE
> ./configure: CHECK_AUTH: command not found  << HERE
> checking for purify... no
> ./configure: CHECK_THREADS: command not found  << HERE
> configure: creating ./config.status
> config.status: creating plplot/Makefile
> config.status: creating plplot/lib/Makefile
> config.status: creating nucleus/Makefile
> config.status: creating ajax/Makefile
> config.status: creating emboss/Makefile
> config.status: creating emboss/acd/Makefile
> config.status: creating test/Makefile
> config.status: creating test/data/Makefile
> config.status: creating test/embl/Makefile
> config.status: creating test/genbank/Makefile
> config.status: creating test/gb/Makefile
> config.status: creating test/pir/Makefile
> config.status: creating test/swiss/Makefile
> config.status: creating test/swnew/Makefile
> config.status: creating test/wormpep/Makefile
> config.status: creating emboss/data/Makefile
> config.status: creating emboss/data/AAINDEX/Makefile
> config.status: creating emboss/data/CODONS/Makefile
> config.status: creating emboss/data/REBASE/Makefile
> config.status: creating emboss/data/PRINTS/Makefile
> config.status: creating emboss/data/PROSITE/Makefile
> config.status: creating doc/Makefile
> config.status: creating doc/manuals/Makefile
> config.status: creating doc/tutorials/Makefile
> config.status: creating doc/programs/Makefile
> config.status: creating doc/programs/html/Makefile
> config.status: creating doc/programs/text/Makefile
> config.status: creating jemboss/Makefile
> config.status: creating jemboss/api/Makefile
> config.status: creating jemboss/api/org/Makefile
> config.status: creating jemboss/api/org/emboss/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/gui/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/gui/filetree/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/gui/form/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/gui/sequenceChooser/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/gui/startup/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/parser/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/parser/acd/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/programs/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/soap/Makefile
> config.status: creating jemboss/images/Makefile
> config.status: creating jemboss/lib/Makefile
> config.status: creating jemboss/lib/axis/Makefile
> config.status: creating jemboss/org/Makefile
> config.status: creating jemboss/org/emboss/Makefile
> config.status: creating jemboss/org/emboss/jemboss/Makefile
> config.status: creating jemboss/org/emboss/jemboss/gui/Makefile
> config.status: creating jemboss/org/emboss/jemboss/gui/filetree/Makefile
> config.status: creating jemboss/org/emboss/jemboss/gui/form/Makefile
> config.status: creating jemboss/org/emboss/jemboss/gui/startup/Makefile
> config.status: creating jemboss/org/emboss/jemboss/gui/sequenceChooser/Makefile
> config.status: creating jemboss/org/emboss/jemboss/parser/Makefile
> config.status: creating jemboss/org/emboss/jemboss/parser/acd/Makefile
> config.status: creating jemboss/org/emboss/jemboss/programs/Makefile
> config.status: creating jemboss/org/emboss/jemboss/server/Makefile
> config.status: creating jemboss/org/emboss/jemboss/soap/Makefile
> config.status: creating jemboss/resources/Makefile
> config.status: creating jemboss/utils/Makefile
> config.status: creating Makefile
> config.status: executing depfiles commands
> #

then when doing 'make'...

> # make
> Making all in plplot
> make[1]: Entering directory `/home/work/EMBOSS/test/plplot'
> Making all in lib
> make[2]: Entering directory `/home/work/EMBOSS/test/plplot/lib'
> make[2]: Nothing to be done for `all'.
> make[2]: Leaving directory `/home/work/EMBOSS/test/plplot/lib'
> make[2]: Entering directory `/home/work/EMBOSS/test/plplot'
> source='pdfutils.c' object='pdfutils.lo' libtool=yes \
> depfile='.deps/pdfutils.Plo' tmpdepfile='.deps/pdfutils.TPlo' \
> depmode=gcc3 /bin/sh ../depcomp \
> /bin/sh ../libtool --mode=compile gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2.6.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1  -I. -I. -I/usr/X11R6/include -I./ -I/usr/include/gd    -g -O2 -c -o pdfutils.lo `test -f pdfutils.c || echo './'`pdfutils.c
> ../libtool: s%^.*/%%: No such file or directory
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> : compile: cannot determine name of library object from `'
> make[2]: *** [pdfutils.lo] Error 1
> make[2]: Leaving directory `/home/work/EMBOSS/test/plplot'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/home/work/EMBOSS/test/plplot'
> make: *** [all-recursive] Error 1
> #

The system is a Redhat 7.3, autoconf 2.13 RPM, automake 1.4p5 RPM
Any hints of what is the problem?
Thanks.

Regards,

martin

-- 
Mart?n Sarachu
mad at biol.unlp.edu.ar
EMBNet Argentina
http://www.ar.embnet.org


From mad at biol.unlp.edu.ar  Tue Feb 24 09:24:10 2004
From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=)
Date: Tue, 24 Feb 2004 11:24:10 -0300
Subject: [EMBOSS] cannot compile a single program
In-Reply-To: <5.2.1.1.1.20040224135709.0315dd68@udcf.gla.ac.uk>
References: <5.2.1.1.1.20040223145844.00acecd0@udcf.gla.ac.uk> <5.2.1.1.1.20040223145844.00acecd0@udcf.gla.ac.uk> <5.2.1.1.1.20040224135709.0315dd68@udcf.gla.ac.uk>
Message-ID: <403B5E8A.8000002@biol.unlp.edu.ar>

Hi

installed libtool-1.5.2 and yet the same errors

Regards,

martin

Derek Gatherer wrote:
> Hi
> 
> You will need libtool as well, by the looks of it.
> http://www.gnu.org/software/libtool/
> 
> Hope this helps
> Derek
> 
> 
> At 09:28 24/02/2004 -0300, you wrote:
> 
>> Hi Derek,
>>
>> thanks for your help. I've got other problems though, I followed your 
>> steps and when doing make I get
>>
>>> # make
>>> Making all in plplot
>>> make[1]: Entering directory `/home/work/EMBOSS/test/plplot'
>>> Making all in lib
>>> make[2]: Entering directory `/home/work/EMBOSS/test/plplot/lib'
>>> make[2]: Nothing to be done for `all'.
>>> make[2]: Leaving directory `/home/work/EMBOSS/test/plplot/lib'
>>> make[2]: Entering directory `/home/work/EMBOSS/test/plplot'
>>> source='pdfutils.c' object='pdfutils.lo' libtool=yes \
>>> depfile='.deps/pdfutils.Plo' tmpdepfile='.deps/pdfutils.TPlo' \
>>> depmode=gcc3 /bin/sh ../depcomp \
>>> /bin/sh ../libtool --mode=compile gcc -DPACKAGE_NAME=\"\" 
>>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
>>> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2.6.0\" 
>>> -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 
>>> -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 
>>> -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 
>>> -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 
>>> -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 
>>> -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 
>>> -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 
>>> -DHAVE_LIBM=1  -I. -I. -I/usr/X11R6/include -I./ -I/usr/include/gd    
>>> -g -O2 -c -o pdfutils.lo `test -f pdfutils.c || echo './'`pdfutils.c
>>> ../libtool: s%^.*/%%: No such file or directory
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> : compile: cannot determine name of library object from `'
>>> make[2]: *** [pdfutils.lo] Error 1
>>> make[2]: Leaving directory `/home/work/EMBOSS/test/plplot'
>>> make[1]: *** [all-recursive] Error 1
>>> make[1]: Leaving directory `/home/work/EMBOSS/test/plplot'
>>> make: *** [all-recursive] Error 1
>>> #
>>
>>
>> Can you help me with this? Thank you.
>>
>>
>> Regards,
>>
>> martin
>>
>>
>> Derek Gatherer wrote:
>>
>>> Hi
>>> You need to be working from the cvs version of emboss:
>>>  >cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss login
>>>  >cvs
>>>  >cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss 
>>> checkout emboss
>>>  >cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss logout
>>> Assuming you have got this, you need to do what you did, ie. add the 
>>> code in the correct place and modify the makefile appropriately, and 
>>> then go to the correct directory and enter:
>>>  >aclocal -I m4
>>>  >autoconf -v
>>>  >automake -a
>>>  >./configure
>>>  >make
>>>  >make check
>>>  >make install
>>>  >make clean
>>> You'll need up to date versions of autoconf and automake.  We add 
>>> lots of local code - it's convoluted to do all this, but it always 
>>> works.
>>> Cheers
>>> Derek
>>> At 11:52 23/02/2004 -0300, you wrote:
>>>
>>>> Dear list,
>>>>
>>>> I'm trying to add a program to our EMBOSS-2.6.0 installation.
>>>> These are the steps I followed:
>>>> - added clustal.c into EMBOSS_distro/emboss dir and clustal.acd 
>>>> under EMBOSS_distro/emboss/acd
>>>> - then edited EMBOSS_distro/emboss/Makefile.am and added 'clustal' 
>>>> to the 'bin_PROGRAMS' section and the line 'clustal_SOURCES = 
>>>> clustal.c' to the same Makefile.am
>>>> - when doing a 'make clustal' into EMBOSS_distro/emboss dir I get this
>>>>
>>>>> # make clustal
>>>>> cd .. && /bin/sh ./config.status emboss/Makefile depfiles
>>>>> config.status: creating emboss/Makefile
>>>>> config.status: executing depfiles commands
>>>>> Makefile:2179: aaindexextract.Po: No such file or directory
>>>>> Makefile:2180: abiview.Po: No such file or directory
>>>>> Makefile:2181: acdc.Po: No such file or directory
>>>>> Makefile:2182: ajtest.Po: No such file or directory
>>>>> Makefile:2183: antigenic.Po: No such file or directory
>>>>> Makefile:2184: backtranseq.Po: No such file or directory
>>>>> Makefile:2185: banana.Po: No such file or directory
>>>>> Makefile:2186: biosed.Po: No such file or directory
>>>>> Makefile:2187: btwisted.Po: No such file or directory
>>>>> Makefile:2188: cai.Po: No such file or directory
>>>>> Makefile:2189: chaos.Po: No such file or directory
>>>>> Makefile:2190: charge.Po: No such file or directory
>>>>> Makefile:2191: checktrans.Po: No such file or directory
>>>>> Makefile:2192: chips.Po: No such file or directory
>>>>> Makefile:2193: cirdna.Po: No such file or directory
>>>>> Makefile:2194: clustal.Po: No such file or directory
>>>>> Makefile:2195: codcmp.Po: No such file or directory
>>>>> Makefile:2196: coderet.Po: No such file or directory
>>>>> Makefile:2197: complex.Po: No such file or directory
>>>>> Makefile:2198: compseq.Po: No such file or directory
>>>>> Makefile:2199: cons.Po: No such file or directory
>>>>> Makefile:2200: corbatest.Po: No such file or directory
>>>>> Makefile:2201: cpgplot.Po: No such file or directory
>>>>> Makefile:2202: cpgreport.Po: No such file or directory
>>>>> Makefile:2203: cusp.Po: No such file or directory
>>>>> Makefile:2204: cutgextract.Po: No such file or directory
>>>>> Makefile:2205: cutseq.Po: No such file or directory
>>>>> Makefile:2206: dan.Po: No such file or directory
>>>>> Makefile:2207: dbiblast.Po: No such file or directory
>>>>> Makefile:2208: dbifasta.Po: No such file or directory
>>>>> Makefile:2209: dbiflat.Po: No such file or directory
>>>>> Makefile:2210: dbigcg.Po: No such file or directory
>>>>> Makefile:2211: degapseq.Po: No such file or directory
>>>>> Makefile:2212: demoalign.Po: No such file or directory
>>>>> Makefile:2213: demofeatures.Po: No such file or directory
>>>>> Makefile:2214: demolist.Po: No such file or directory
>>>>> Makefile:2215: demoreport.Po: No such file or directory
>>>>> Makefile:2216: demosequence.Po: No such file or directory
>>>>> Makefile:2217: demostring.Po: No such file or directory
>>>>> Makefile:2218: demotable.Po: No such file or directory
>>>>> Makefile:2219: descseq.Po: No such file or directory
>>>>> Makefile:2220: diffseq.Po: No such file or directory
>>>>> Makefile:2221: digest.Po: No such file or directory
>>>>> Makefile:2222: distmat.Po: No such file or directory
>>>>> Makefile:2223: dotmatcher.Po: No such file or directory
>>>>> Makefile:2224: dotpath.Po: No such file or directory
>>>>> Makefile:2225: dottup.Po: No such file or directory
>>>>> Makefile:2226: dreg.Po: No such file or directory
>>>>> Makefile:2227: einverted.Po: No such file or directory
>>>>> Makefile:2228: embossdata.Po: No such file or directory
>>>>> Makefile:2229: embossversion.Po: No such file or directory
>>>>> Makefile:2230: emma.Po: No such file or directory
>>>>> Makefile:2231: emowse.Po: No such file or directory
>>>>> Makefile:2232: entrails.Po: No such file or directory
>>>>> Makefile:2233: entret.Po: No such file or directory
>>>>> Makefile:2234: eprimer3.Po: No such file or directory
>>>>> Makefile:2235: equicktandem.Po: No such file or directory
>>>>> Makefile:2236: est2genome.Po: No such file or directory
>>>>> Makefile:2237: etandem.Po: No such file or directory
>>>>> Makefile:2238: extractfeat.Po: No such file or directory
>>>>> Makefile:2239: extractseq.Po: No such file or directory
>>>>> Makefile:2240: findkm.Po: No such file or directory
>>>>> Makefile:2241: freak.Po: No such file or directory
>>>>> Makefile:2242: fuzznuc.Po: No such file or directory
>>>>> Makefile:2243: fuzzpro.Po: No such file or directory
>>>>> Makefile:2244: fuzztran.Po: No such file or directory
>>>>> Makefile:2245: garnier.Po: No such file or directory
>>>>> Makefile:2246: geecee.Po: No such file or directory
>>>>> Makefile:2247: getorf.Po: No such file or directory
>>>>> Makefile:2248: helixturnhelix.Po: No such file or directory
>>>>> Makefile:2249: histogramtest.Po: No such file or directory
>>>>> Makefile:2250: hmoment.Po: No such file or directory
>>>>> Makefile:2251: iep.Po: No such file or directory
>>>>> Makefile:2252: infoalign.Po: No such file or directory
>>>>> Makefile:2253: infoseq.Po: No such file or directory
>>>>> Makefile:2254: intconv.Po: No such file or directory
>>>>> Makefile:2255: isochore.Po: No such file or directory
>>>>> Makefile:2256: jembossctl.Po: No such file or directory
>>>>> Makefile:2257: lindna.Po: No such file or directory
>>>>> Makefile:2258: listor.Po: No such file or directory
>>>>> Makefile:2259: marscan.Po: No such file or directory
>>>>> Makefile:2260: maskfeat.Po: No such file or directory
>>>>> Makefile:2261: maskseq.Po: No such file or directory
>>>>> Makefile:2262: matcher.Po: No such file or directory
>>>>> Makefile:2263: megamerger.Po: No such file or directory
>>>>> Makefile:2264: merger.Po: No such file or directory
>>>>> Makefile:2265: msbar.Po: No such file or directory
>>>>> Makefile:2266: mwcontam.Po: No such file or directory
>>>>> Makefile:2267: mwfilter.Po: No such file or directory
>>>>> Makefile:2268: needle.Po: No such file or directory
>>>>> Makefile:2269: newcpgreport.Po: No such file or directory
>>>>> Makefile:2270: newcpgseek.Po: No such file or directory
>>>>> Makefile:2271: newseq.Po: No such file or directory
>>>>> Makefile:2272: noreturn.Po: No such file or directory
>>>>> Makefile:2273: notseq.Po: No such file or directory
>>>>> Makefile:2274: nthseq.Po: No such file or directory
>>>>> Makefile:2275: octanol.Po: No such file or directory
>>>>> Makefile:2276: oddcomp.Po: No such file or directory
>>>>> Makefile:2277: palindrome.Po: No such file or directory
>>>>> Makefile:2278: pasteseq.Po: No such file or directory
>>>>> Makefile:2279: patmatdb.Po: No such file or directory
>>>>> Makefile:2280: patmatmotifs.Po: No such file or directory
>>>>> Makefile:2281: patmattest.Po: No such file or directory
>>>>> Makefile:2282: pepcoil.Po: No such file or directory
>>>>> Makefile:2283: pepinfo.Po: No such file or directory
>>>>> Makefile:2284: pepnet.Po: No such file or directory
>>>>> Makefile:2285: pepstats.Po: No such file or directory
>>>>> Makefile:2286: pepwheel.Po: No such file or directory
>>>>> Makefile:2287: pepwindow.Po: No such file or directory
>>>>> Makefile:2288: pepwindowall.Po: No such file or directory
>>>>> Makefile:2289: pestfind.Po: No such file or directory
>>>>> Makefile:2290: plotcon.Po: No such file or directory
>>>>> Makefile:2291: plotorf.Po: No such file or directory
>>>>> Makefile:2292: polydot.Po: No such file or directory
>>>>> Makefile:2293: preg.Po: No such file or directory
>>>>> Makefile:2294: prettyplot.Po: No such file or directory
>>>>> Makefile:2295: prettyseq.Po: No such file or directory
>>>>> Makefile:2296: prima.Po: No such file or directory
>>>>> Makefile:2297: primers.Po: No such file or directory
>>>>> Makefile:2298: primersearch.Po: No such file or directory
>>>>> Makefile:2299: printsextract.Po: No such file or directory
>>>>> Makefile:2300: profit.Po: No such file or directory
>>>>> Makefile:2301: prophecy.Po: No such file or directory
>>>>> Makefile:2302: prophet.Po: No such file or directory
>>>>> Makefile:2303: prosextract.Po: No such file or directory
>>>>> Makefile:2304: pscan.Po: No such file or directory
>>>>> Makefile:2305: rebaseextract.Po: No such file or directory
>>>>> Makefile:2306: recoder.Po: No such file or directory
>>>>> Makefile:2307: redata.Po: No such file or directory
>>>>> Makefile:2308: remap.Po: No such file or directory
>>>>> Makefile:2309: restover.Po: No such file or directory
>>>>> Makefile:2310: restrict.Po: No such file or directory
>>>>> Makefile:2311: revseq.Po: No such file or directory
>>>>> Makefile:2312: seealso.Po: No such file or directory
>>>>> Makefile:2313: seqinfo.Po: No such file or directory
>>>>> Makefile:2314: seqmatchall.Po: No such file or directory
>>>>> Makefile:2315: seqret.Po: No such file or directory
>>>>> Makefile:2316: seqretall.Po: No such file or directory
>>>>> Makefile:2317: seqretallfeat.Po: No such file or directory
>>>>> Makefile:2318: seqretset.Po: No such file or directory
>>>>> Makefile:2319: seqretsingle.Po: No such file or directory
>>>>> Makefile:2320: seqretsplit.Po: No such file or directory
>>>>> Makefile:2321: showalign.Po: No such file or directory
>>>>> Makefile:2322: showdb.Po: No such file or directory
>>>>> Makefile:2323: showfeat.Po: No such file or directory
>>>>> Makefile:2324: showorf.Po: No such file or directory
>>>>> Makefile:2325: showseq.Po: No such file or directory
>>>>> Makefile:2326: shuffleseq.Po: No such file or directory
>>>>> Makefile:2327: sigcleave.Po: No such file or directory
>>>>> Makefile:2328: silent.Po: No such file or directory
>>>>> Makefile:2329: sirna.Po: No such file or directory
>>>>> Makefile:2330: sixpack.Po: No such file or directory
>>>>> Makefile:2331: skipseq.Po: No such file or directory
>>>>> Makefile:2332: splitter.Po: No such file or directory
>>>>> Makefile:2333: stretcher.Po: No such file or directory
>>>>> Makefile:2334: stssearch.Po: No such file or directory
>>>>> Makefile:2335: supermatcher.Po: No such file or directory
>>>>> Makefile:2336: syco.Po: No such file or directory
>>>>> Makefile:2337: testplot.Po: No such file or directory
>>>>> Makefile:2338: textsearch.Po: No such file or directory
>>>>> Makefile:2339: tfextract.Po: No such file or directory
>>>>> Makefile:2340: tfm.Po: No such file or directory
>>>>> Makefile:2341: tfscan.Po: No such file or directory
>>>>> Makefile:2342: tmap.Po: No such file or directory
>>>>> Makefile:2343: tranalign.Po: No such file or directory
>>>>> Makefile:2344: transeq.Po: No such file or directory
>>>>> Makefile:2345: treetypedisplay.Po: No such file or directory
>>>>> Makefile:2346: trimest.Po: No such file or directory
>>>>> Makefile:2347: trimseq.Po: No such file or directory
>>>>> Makefile:2348: twofeat.Po: No such file or directory
>>>>> Makefile:2349: union.Po: No such file or directory
>>>>> Makefile:2350: vectorstrip.Po: No such file or directory
>>>>> Makefile:2351: water.Po: No such file or directory
>>>>> Makefile:2352: whichdb.Po: No such file or directory
>>>>> Makefile:2353: wobble.Po: No such file or directory
>>>>> Makefile:2354: wordcount.Po: No such file or directory
>>>>> Makefile:2355: wordmatch.Po: No such file or directory
>>>>> Makefile:2356: wossname.Po: No such file or directory
>>>>> Makefile:2357: yank.Po: No such file or directory
>>>>> make: *** No rule to make target `yank.Po'.  Stop.
>>>>> #
>>>>
>>>>
>>>>
>>>> What am I missing?
>>>>
>>>> Regards,
>>>>
>>>> martin
>>>>
>>>> -- 
>>>> Mart?n Sarachu
>>>> mad at biol.unlp.edu.ar
>>>> EMBNet Argentina
>>>> http://www.ar.embnet.org
>>>
>>>
>>
>> -- 
>> Mart?n Sarachu
>> mad at biol.unlp.edu.ar
>> EMBNet Argentina
>> http://www.ar.embnet.org
> 
> 
> 

-- 
Mart?n Sarachu
mad at biol.unlp.edu.ar
EMBNet Argentina
http://www.ar.embnet.org


From pmr at ebi.ac.uk  Tue Feb 24 09:31:35 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Tue, 24 Feb 2004 14:31:35 +0000
Subject: [EMBOSS] cannot compile a single program
In-Reply-To: <403B5E8A.8000002@biol.unlp.edu.ar>
References: <5.2.1.1.1.20040223145844.00acecd0@udcf.gla.ac.uk> <5.2.1.1.1.20040223145844.00acecd0@udcf.gla.ac.uk> <5.2.1.1.1.20040224135709.0315dd68@udcf.gla.ac.uk> <403B5E8A.8000002@biol.unlp.edu.ar>
Message-ID: <403B6047.80001@ebi.ac.uk>

Mart?n Sarachu wrote:

> Hi
> 
> installed libtool-1.5.2 and yet the same errors
>>>> /bin/sh ../libtool --mode=compile gcc -DPACKAGE_NAME=\"\" 
>>>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
>>>> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2.6.0\" 
>>>> -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 
>>>> -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 
>>>> -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 
>>>> -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 
>>>> -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 
>>>> -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 
>>>> -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 
>>>> -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1  -I. -I. -I/usr/X11R6/include -I./ 
>>>> -I/usr/include/gd    -g -O2 -c -o pdfutils.lo `test -f pdfutils.c || 
>>>> echo './'`pdfutils.c
>>>> ../libtool: s%^.*/%%: No such file or directory
>>>> ../libtool: -e: command not found

The EMBOSS README file suggests:

On some systems there may be compatibility problems with different
automake, autoconf or libtool versions. Always make sure that you keep
up to date with releases of these tools and let us know of any
problems you experience (emboss-bug at embnet.org). If a libtool problem
does arise you can try deleting the following files:

    config.cache
    ltmain.sh
    ltconfig
    libtool

and then type

    aclocal -I m4
    autoconf
    automake -a

and then retry the make.


But I have to wonder whether you are using the CVS version of the code 
... that "-DVERSION=2.6.0" does not look right!!!!!

For the current CVS it is 2.9.0 (although we will be making a 2.8.1 
release soon).

Also, for one-off programs, I plan to add a "myemboss" EMBASSY directory 
to EMBOSS 2.9.0 with instructions for compiling your own local programs.

Hope this helps,

Peter Rice



From mad at biol.unlp.edu.ar  Tue Feb 24 09:45:45 2004
From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=)
Date: Tue, 24 Feb 2004 11:45:45 -0300
Subject: [EMBOSS] cannot compile a single program
In-Reply-To: <403B6047.80001@ebi.ac.uk>
References: <5.2.1.1.1.20040223145844.00acecd0@udcf.gla.ac.uk> <5.2.1.1.1.20040223145844.00acecd0@udcf.gla.ac.uk> <5.2.1.1.1.20040224135709.0315dd68@udcf.gla.ac.uk> <403B5E8A.8000002@biol.unlp.edu.ar> <403B6047.80001@ebi.ac.uk>
Message-ID: <403B6399.5010100@biol.unlp.edu.ar>

CVS version is still downloading... :)

I'm trying to add some programs to our current emboss version (2.6.0) so I'm 
working under the distribution directory of EMBOSS-2.6.0
I've added BLAST and FASTA wrappers without any trouble by adding entries in 
emboss/Makefile.am and doing a 'make blast_wrapper'

Peter Rice wrote:
> Mart?n Sarachu wrote:
> 
>> Hi
>>
>> installed libtool-1.5.2 and yet the same errors
>>
>>>>> /bin/sh ../libtool --mode=compile gcc -DPACKAGE_NAME=\"\" 
>>>>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
>>>>> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2.6.0\" 
>>>>> -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 
>>>>> -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 
>>>>> -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 
>>>>> -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 
>>>>> -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 
>>>>> -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 
>>>>> -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 
>>>>> -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1  -I. -I. -I/usr/X11R6/include -I./ 
>>>>> -I/usr/include/gd    -g -O2 -c -o pdfutils.lo `test -f pdfutils.c 
>>>>> || echo './'`pdfutils.c
>>>>> ../libtool: s%^.*/%%: No such file or directory
>>>>> ../libtool: -e: command not found
> 
> 
> The EMBOSS README file suggests:
> 
> On some systems there may be compatibility problems with different
> automake, autoconf or libtool versions. Always make sure that you keep
> up to date with releases of these tools and let us know of any
> problems you experience (emboss-bug at embnet.org). If a libtool problem
> does arise you can try deleting the following files:
> 
>    config.cache
>    ltmain.sh
>    ltconfig
>    libtool
> 
> and then type
> 
>    aclocal -I m4
>    autoconf
>    automake -a
> 
> and then retry the make.
> 
> 
> But I have to wonder whether you are using the CVS version of the code 
> ... that "-DVERSION=2.6.0" does not look right!!!!!
> 
> For the current CVS it is 2.9.0 (although we will be making a 2.8.1 
> release soon).
> 
> Also, for one-off programs, I plan to add a "myemboss" EMBASSY directory 
> to EMBOSS 2.9.0 with instructions for compiling your own local programs.
> 
> Hope this helps,
> 
> Peter Rice
> 

-- 
Mart?n Sarachu
mad at biol.unlp.edu.ar
EMBNet Argentina
http://www.ar.embnet.org


From a.garcia at imb.uq.edu.au  Wed Feb 25 08:35:27 2004
From: a.garcia at imb.uq.edu.au (a.garcia at imb.uq.edu.au)
Date: Wed, 25 Feb 2004 23:35:27 +1000
Subject: [EMBOSS] pipelines/wflows/PISE
Message-ID: <web-3883384@imb.uq.edu.au>

G-PIPE is a work flow generator for PISE/EMBOSS. It allows 
users to easily define and monitor work flows (in-silicon) 
experiments. Once the work flows have been defined (steps, 
parameters, conditions) users can save them as XML files 
and share them across different GPIPE installations. Users 
can also distribute different works with in a work flow 
across different servers around a grid. 

This is the first official release of GPIPE, we hope to 
improve on a later release. We appreciate your comments. 

The server where GPIPE is in the moment 
(http://sirio.sanmartin.edu.co/Pise/gpipe.html)does not 
allow run complex work flows (computing demanding) but is 
enough  to exemplify GPIPE's capacities. Information is 
also available at 
http://www.pasteur.fr/recherche/unites/sis/Pise/#


From d.m.a.martin at dundee.ac.uk  Wed Feb 25 10:33:09 2004
From: d.m.a.martin at dundee.ac.uk (David Martin)
Date: Wed, 25 Feb 2004 15:33:09 +0000
Subject: [EMBOSS] Adding new programs on OS X - aclocal problem
Message-ID: <BC6270B5.E787%d.m.a.martin@dundee.ac.uk>

I have been trying to add some local code in to EMBOSS on OS X. I have the
latest and greatest autoconf and automake. Iget problems with aclocal as:

% aclocal -I m4
aclocal: couldn't open directory `m4': No such file or directory

and % aclocal
aclocal: configure.in: 140: macro `AM_PROG_LIBTOOL' not found in library

Any suggestions or do I have to do some manual hacking of the various
configure scripts?

..d



From d.m.a.martin at dundee.ac.uk  Wed Feb 25 12:01:21 2004
From: d.m.a.martin at dundee.ac.uk (David Martin)
Date: Wed, 25 Feb 2004 17:01:21 +0000
Subject: [EMBOSS] More OS X woes
Message-ID: <BC628561.E79E%d.m.a.martin@dundee.ac.uk>

OK, I have now tried the cvs version of EMBOSS.

aclocal -I m4 runs without errors

Autoconf fails with:
% autoconf -v
... bits snipped ...
autom4te: creating configure
autom4te: formatting traces for `/tmp/am4txD3aAT/patterns':
m4_pattern_allow, m4_pattern_forbid
autom4te: forbidden tokens: ^_?A[CHUM]_|_AC_|^LIBOBJS$|^_?m4_|^dnl$|^_?AS_
autom4te: forbidden token : ^LIBOBJS$ => do not use LIBOBJS directly, use
AC_LIBOBJ (see section `AC_LIBOBJ vs LIBOBJS'
autom4te: allowed   tokens: ^AM_[A-Z]+FLAGS$|^AS_FLAGS$
configure.in:151: error: possibly undefined macro: AC_PROG_LIBTOOL
      If this token and others are legitimate, please use m4_pattern_allow.
      See the Autoconf documentation.


Any thoughts?

..d



From pmr at ebi.ac.uk  Wed Feb 25 12:10:54 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Wed, 25 Feb 2004 17:10:54 +0000
Subject: [EMBOSS] More OS X woes
In-Reply-To: <BC628561.E79E%d.m.a.martin@dundee.ac.uk>
References: <BC628561.E79E%d.m.a.martin@dundee.ac.uk>
Message-ID: <403CD71E.7030000@ebi.ac.uk>

David Martin wrote:

> OK, I have now tried the cvs version of EMBOSS.
> 
> aclocal -I m4 runs without errors
> 
> Autoconf fails with:
> % autoconf -v
> ... bits snipped ...

> Any thoughts?

autoconf does that for me too ... but without the -v it is perfectly happy.

Followups to emboss-bug, please!

Peter



From jmarken at trubion.com  Thu Feb 26 19:50:39 2004
From: jmarken at trubion.com (John Marken)
Date: Thu, 26 Feb 2004 16:50:39 -0800
Subject: [EMBOSS] jemboss rebase etc can't utilize embossre.enz file
Message-ID: <c98c78e91e13524ca8c66dc7243ef5a0403e9462@genecraft.com>

Hello,
Just installed jemboss, the interface works but programs needing database files like remap don't work. Remap can return the sequence and translations but no restriction enzyme sites are shown, nor are there enzymes listed the cuts or no cut sections of the resulting file. Command line emboss is working and  remap can find the rebase (embossre.enz etc)  files as specified in the .embossrc in //usr/local/emboss/share/EMBOSS/data/REBASE.

The jemboss.properties file in
"//usr/local/jakarta-tomcat-4.1.29/webapps/axis/WEB-INF/classes/resources"
contains the line 
"embossData=/usr/local/emboss/share/EMBOSS/data/" (without quotes)

Is the jemboss.propterties file in the right place? Is there another config file that needs editing?

Regards
John Marken


Trubion Pharmaceuticals Inc.
2401 4th Ave. Suite 1050
Seattle, WA 98121
206-838-0500




From jmarken at trubion.com  Fri Feb 27 14:04:34 2004
From: jmarken at trubion.com (John Marken)
Date: Fri, 27 Feb 2004 11:04:34 -0800
Subject: [EMBOSS] jemboss rebase etc can't utilize embossre.enz file
Message-ID: <24080b25f20f0ebe98ed200caebb3b1d403f94c4@genecraft.com>


Thank you. There indeed was another copy of jemboss.properties in the home directory for the tomcat server owner. And it actually is important to not install  the server as root:>)

John
-----Original Message-----
From: Dr T. Carver [mailto:tcarver at rfcgr.mrc.ac.uk]
Sent: Friday, February 27, 2004 2:25 AM
To: John Marken
Subject: Re: [EMBOSS] jemboss rebase etc can't utilize embossre.enz file


Hi John

This looks to be the correct jemboss.properties (just ensure there isn't
one in the home directory of the tomcat user).

Did you run 'rebaseextract'?

What does the rest of the jemboss.properties look like?

Regards
Tim

Tim Carver
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494500  Fax: +44 1223 494512
E-mail: tcarver at rfcgr.mrc.ac.uk  Web: http://www.rfcgr.mrc.ac.uk


On Thu, 26 Feb 2004, John Marken wrote:

> Hello,
> Just installed jemboss, the interface works but programs needing database files like remap don't work. Remap can return the sequence and translations but no restriction enzyme sites are shown, nor are there enzymes listed the cuts or no cut sections of the resulting file. Command line emboss is working and  remap can find the rebase (embossre.enz etc)  files as specified in the .embossrc in //usr/local/emboss/share/EMBOSS/data/REBASE.
>
> The jemboss.properties file in
> "//usr/local/jakarta-tomcat-4.1.29/webapps/axis/WEB-INF/classes/resources"
> contains the line
> "embossData=/usr/local/emboss/share/EMBOSS/data/" (without quotes)
>
> Is the jemboss.propterties file in the right place? Is there another config file that needs editing?
>
> Regards
> John Marken
>
>
> Trubion Pharmaceuticals Inc.
> 2401 4th Ave. Suite 1050
> Seattle, WA 98121
> 206-838-0500
>
>




From ouse_ser_magro at ig.com.br  Fri Feb 27 14:27:01 2004
From: ouse_ser_magro at ig.com.br (Carujo,,)
Date: Fri, 27 Feb 2004 19:27:01 +0000 (GMT)
Subject: [EMBOSS] RE, respuesta..
Message-ID: <20040227192701.AEDEA7D110@mercury.hgmp.mrc.ac.uk>

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From fmachadoj at inf.ufrgs.br  Sun Feb 15 13:19:29 2004
From: fmachadoj at inf.ufrgs.br (Fernando Machado)
Date: Sun, 15 Feb 2004 10:19:29 -0300
Subject: [EMBOSS] auth using jemboss
Message-ID: <402F71E1.60706@inf.ufrgs.br>

I?m having trouble using jemboss. evrth was fine, but authentication 
stopped working. Now I cant authenticate anymore.
do somebody knows what can i do?

thanks

Fernando Machado
UFRGS - II - 43424



From MAILER-DAEMON at tank.uams.edu  Wed Feb  4 15:13:52 2004
From: MAILER-DAEMON at tank.uams.edu (MAILER-DAEMON at tank.uams.edu)
Date: Wed, 04 Feb 2004 09:13:52 -0600
Subject: [EMBOSS] Undeliverable mail: 
Message-ID: <receipt-77613715@tank.uams.edu>

Failed to deliver to '<childsgwenv at exchange.uams.edu>'
RAV AntiVirus plugin for CommuniGate Pro has found a virus in the e-mail you are about to send. Your message is not delivered.

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From dsullivan at gradipore.com  Wed Feb  4 18:42:17 2004
From: dsullivan at gradipore.com (Dan Sullivan)
Date: Thu, 5 Feb 2004 05:42:17 +1100 
Subject: [EMBOSS] 18 Month Shelf Life and Free Buffer
Message-ID: <017AE08058A1D3118A7B0008C70D6217030116FA@GSYD_NT5>

 
 
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From postmaster at eva.mpg.de  Wed Feb  4 23:38:45 2004
From: postmaster at eva.mpg.de (postmaster at eva.mpg.de)
Date: Thu,  5 Feb 2004 00:38:45 +0100 (CET)
Subject: [EMBOSS] VIRUS IN YOUR MAIL
Message-ID: <20040204233845.2421A206B8@email.eva.mpg.de>

                           V I R U S  A L E R T

Our viruschecker found the

	W32/Mydoom.a at MM

virus(es) in your email to the following recipient(s):

-> stoneking at eva.mpg.de

Please check your system for viruses, or ask your system administrator
to do so.
#
For your reference, here are the headers from your email:

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From: emboss at embnet.org
To: stoneking at eva.mpg.de
Subject: Error
Date: Wed, 4 Feb 2004 17:44:04 -0600
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From newsletter at prographicssportswear.com  Thu Feb  5 17:36:34 2004
From: newsletter at prographicssportswear.com (newsletter at prographicssportswear.com)
Date: Thu, 5 Feb 2004 12:36:34 -0500
Subject: [EMBOSS] Please send this email to your T-shirt ordering committee
Message-ID: <200402051736.i15HaYh08277@www.prographicssportswear.com>

You must use an HTML compliant e-mail client to view this message properly.

Visit http://www.prographicssportswear.com for more information.
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From aengus.stewart at cancer.org.uk  Thu Feb  5 18:44:06 2004
From: aengus.stewart at cancer.org.uk (Aengus Stewart)
Date: Thu, 05 Feb 2004 18:44:06 +0000
Subject: [EMBOSS] dbifasta possible problem
In-Reply-To: <20040130153412.E6096@uracil.uio.no>
References: <20040130153412.E6096@uracil.uio.no>
Message-ID: <40228EF6.5080108@cancer.org.uk>


I have been using Warren Gish's nrdb2 to create a non-redundant protein dataset

It generates FASTA title lines like

>swiss:ACDD_METMA Q8PRQ5 Acetyl-CoA decarbonylase/synthase complex delta subunit (ACDS complex delta subunit) (Corrinoid/iron-sulfur component small subunit).
trembl:Q8PRQ5 Q8PRQ5 CO dehydrogenase/acetyl-COA synthase delta subunit (EC 1.2.99.2).
refseqp:NP_632712 NP_632712 Methanosarcina mazei Goe1 CO dehydrogenase/acetyl-COA synthase delta subunit [Methanosarcina mazei Goe1]. 0/0
refseqp:NP_634109 NP_634109 Methanosarcina mazei Goe1 CO dehydrogenase/acetyl-COA synthase delta subunit [Methanosarcina mazei Goe1]. 0/0

Where it cats together the titles from the different DBs that have identical entries.

I have discovered that dbifasta will only accept -idformat simple to process this file

I assumed I could use -idformat gcgidacc

but this and any other -idformat bar simple causes dbifasta to "finish"

I say finish as there is no errors or complaints it just ends...........

I didnt expect this, is this correct behaviour?


Cheers
Aengus


-- 
----------------------------------------------------------------------------
Aengus Stewart
Group Leader
Computational Genome Analysis Laboratory  Tel: +44 (0)20 7269 3679
Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
----------------------------------------------------------------------------


From postmaster at wisair.com  Thu Feb  5 20:17:25 2004
From: postmaster at wisair.com (postmaster at wisair.com)
Date: Thu, 5 Feb 2004 22:17:25 +0200
Subject: [EMBOSS] Delivery Status Notification (Failure)
Message-ID: <0qd0HWTUX000009b5@wis.wisair.com>

This is an automatically generated Delivery Status Notification.

Delivery to the following recipients failed.

       dave at wisair.com



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From flavio.licciulli at ba.itb.cnr.it  Fri Feb  6 11:15:08 2004
From: flavio.licciulli at ba.itb.cnr.it (Vito Flavio Licciulli)
Date: Fri, 06 Feb 2004 12:15:08 +0100
Subject: [EMBOSS] dbiflat problem on TRU64
Message-ID: <5.1.0.14.0.20040206120037.045c7d80@area.ba.cnr.it>

I have a problem with dat database entries indexing with dbiflat. Sometimes 
the found entries are different from searched entries .

When I run for example:
$>seqret embl:u18650
Reads and writes (returns) sequences
Output sequence [rg9401257.fasta]:
$>more rg9401257.fasta
RG9401257 AJ401257.1 Rotavirus G9 partial VP7 gene for outer capside glycoprote
in, strain G9P[8], isolate 414/98
attatggaattaaatttaccgatcactggctccatggatacagcatatgcaaattcatca....

The search entry (u18650) comes from ROD division while the entry found 
comes from VRL division.
This is the embl definition in emboss.defaults:
DB embl [ type: N method: emblcd
                format: embl dir: $emboss_db_embl indexdir: 
$emboss_db_embl/INDEX
                exclude: *.dat  file: *.dat  comment: "EMBL sequences"]

I found the same problem in SWISSPROT too.

We have a Compaq TRU64Unix 5.1a, is something related to the dbiflat for 
this OS (sort problem,....) ? or what else?

Regards
         Flavio Licciulli

Vito Flavio Licciulli                          e-mail: 
flavio.licciulli at ba.itb.cnr.it
System & Database Administrator
Italian EMBnet Node
C.N.R. - ITB Sez.di BARI                Phone (39) 080-5482100/30
Via Amendola 168/5  BARI ITALY    Fax   (39) 080-5482607
----------------------------------------------------------------------------




From MAILER-DAEMON at pimail.pi-india.net  Mon Feb  9 10:37:20 2004
From: MAILER-DAEMON at pimail.pi-india.net (MAILER-DAEMON at pimail.pi-india.net)
Date: 9 Feb 2004 10:37:20 -0000
Subject: [EMBOSS] failure notice
Message-ID: <20040209100535.4E8727DDD9@mercury.hgmp.mrc.ac.uk>

Hi. This is the qmail-send program at pimail.pi-india.net.
I'm afraid I wasn't able to deliver your message to the following addresses.
This is a permanent error; I've given up. Sorry it didn't work out.

<brenda at yahoo.co.uk>:
195.50.106.7 does not like recipient.
Remote host said: 553 VS10-RT Possible forgery or deactivated due to abuse (#5.1.1)
Giving up on 195.50.106.7.

--- Below this line is a copy of the message.

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From: emboss at embnet.org
To: brenda at yahoo.co.uk
Subject: HELLO
Date: Mon, 9 Feb 2004 15:37:28 +0530
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------=_NextPart_000_0006_B1AA88D5.B26A025E--




From emeasmex at Roche.COM  Mon Feb  9 10:07:22 2004
From: emeasmex at Roche.COM (emeasmex at Roche.COM)
Date: Mon, 09 Feb 2004 11:07:22 +0100
Subject: [EMBOSS] [MailServer Notification]To Recipient virus found and action taken.
Message-ID: <0b0f01c3eef4$82712570$5c2af591@emea.roche.com>

ScanMail for Microsoft Exchange has detected virus-infected attachment(s).

Sender = owner-emboss at hgmp.mrc.ac.uk
Recipient(s) = emboss at embnet.org
Subject = [EMBOSS] failure notice
Scanning time = 2/9/2004 11:07:22 AM
Engine/Pattern = 6.810-1005/757

Action on virus found:
The message body contains PE_ELKERN.D virus. ScanMail has deleted the message body.

Warning to recipient. ScanMail has detected a virus.


From ".BE.ADM.BE2307.SHG_GATEWAY" at schering.de  Mon Feb  9 10:06:43 2004
From: ".BE.ADM.BE2307.SHG_GATEWAY" at schering.de (".BE.ADM.BE2307.SHG_GATEWAY" at schering.de)
Date: Mon, 9 Feb 2004 11:06:43 +0100
Subject: Virus Alert - ScanMail for Lotus Notes --> [EMBOSS] failure notice
Message-ID: <OFF13B927A.EDB56FA2-ONC1256E35.00378C01@eu.schering.net>

The virus protection system has detected and removed a virus in your email.


Date: 02/09/2004 11:06:43 AM
121:  [EMBOSS] failure notice
Virus:      PE_ELKERN.D
File: document.zip
From: owner-emboss at hgmp.mrc.ac.uk
To:   emboss at embnet.org
Action:     Uncleanable, Quarantined;

Scanned by ScanMail for Lotus Notes 2.51
with scanengine 6.510-1002
and patternfile lpt$vpn.757




From emboss at embnet.org  Tue Feb 10 06:33:32 2004
From: emboss at embnet.org (emboss at embnet.org)
Date: Tue, 10 Feb 2004 12:03:32 +0530
Subject: [EMBOSS] Returned due to virus; was: hello
Message-ID: <200402100634.i1A6YEXE245854@fserv1.yokohama-cu.ac.jp>



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.open-bio.org/pipermail/emboss/attachments/20040210/8b25d728/attachment.htm>

From stefanielager at fastmail.ca  Fri Feb 13 07:54:53 2004
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Fri, 13 Feb 2004 07:54:53 +0000 (UTC)
Subject: [EMBOSS] Database access external app
Message-ID: <20040213075454.D402D86194C@mail.interchange.ca>

Hi,

I'm trying to retrieve entries in EMBOSS using fastacmd as an external
application. It works nice as long as the database, indexed with
formatdb, is a singe fasta file. But when I have big databases that are
split up in volumes and use a .nal file with the names of the idividual
files it doesn't work with EMBOSS anymore. Does anyone have experience
with fastacmd and EMBOSS database indexing in combination with databases
split into volumes?

Stefanie 
_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians


From Marc.Logghe at devgen.com  Fri Feb 13 08:15:59 2004
From: Marc.Logghe at devgen.com (Marc Logghe)
Date: Fri, 13 Feb 2004 09:15:59 +0100
Subject: [EMBOSS] Database access external app
Message-ID: <BEE28BF86078B6429D6C780635718E21904B88@morelia.be.devgen.com>

Hi Stefanie,
Can you show the actual entry in your emboss.default file, or eventual error messages when running the emboss command ?
We use exactly the same system for the worm chromosomal sequences for instance. Every chromosome is a separate blastable 'database'. worm_chromosomes.nal makes them look like 1 big.
The entry looks like this:
DB worm_chromosomes [
   type: N
   format: ncbi
   method: app
   app: "fastacmd -d worm_chromosomes -s %s"
]

HTH,
Marc

> -----Original Message-----
> From: Stefanie Lager [mailto:stefanielager at fastmail.ca]
> Sent: vrijdag 13 februari 2004 8:55
> To: emboss at embnet.org
> Subject: [EMBOSS] Database access external app
> 
> 
> Hi,
> 
> I'm trying to retrieve entries in EMBOSS using fastacmd as an external
> application. It works nice as long as the database, indexed with
> formatdb, is a singe fasta file. But when I have big 
> databases that are
> split up in volumes and use a .nal file with the names of the 
> idividual
> files it doesn't work with EMBOSS anymore. Does anyone have experience
> with fastacmd and EMBOSS database indexing in combination 
> with databases
> split into volumes?
> 
> Stefanie 
> _________________________________________________________________
>     http://fastmail.ca/ - Fast Secure Web Email for Canadians
> 


From stefanielager at fastmail.ca  Fri Feb 13 08:53:19 2004
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Fri, 13 Feb 2004 08:53:19 +0000 (UTC)
Subject: [EMBOSS] Database access external app
In-Reply-To: <BEE28BF86078B6429D6C780635718E21904B88@morelia.be.devgen.com>
Message-ID: <20040213085320.4F6E7863CFF@mail.interchange.ca>

Marc,

I use the same setup as you "app: "fastacmd -d hs_pub_genomic -s %s",
and I try to retrive from a human genome database (each chr is a BIG
fasta file). The formatdb indexing seems OK, fastacmd works on
commandline. But I don't get any error from EMBOSS it just can't retrive
entries (it just hangs there forever). 

Stefanie

> Hi Stefanie,
> Can you show the actual entry in your emboss.default file, or eventual
> error messages when running the emboss command ? We use exactly the
> same system for the worm chromosomal sequences for instance. Every
> chromosome is a separate blastable 'database'. worm_chromosomes.nal
> makes them look like 1 big. The entry looks like this: DB
> worm_chromosomes [ type: N format: ncbi
> method: app
> app: "fastacmd -d worm_chromosomes -s %s"
> ]
> 
> HTH,
> Marc
> 
>> -----Original Message-----
>> From: Stefanie Lager [mailto:stefanielager at fastmail.ca]
>> Sent: vrijdag 13 februari 2004 8:55
>> To: emboss at embnet.org
>> Subject: [EMBOSS] Database access external app
>> 
>> 
>> Hi,
>> 
>> I'm trying to retrieve entries in EMBOSS using fastacmd as an
>> external application. It works nice as long as the database, indexed
>> with formatdb, is a singe fasta file. But when I have big
>> databases that are
>> split up in volumes and use a .nal file with the names of the
>> idividual
>> files it doesn't work with EMBOSS anymore. Does anyone have
>> experience with fastacmd and EMBOSS database indexing in combination
>> with databases
>> split into volumes?
>> 
>> Stefanie
>> _________________________________________________________________
>> http://fastmail.ca/ - Fast Secure Web Email for Canadians
>> 
_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians


From Marc.Logghe at devgen.com  Fri Feb 13 09:43:55 2004
From: Marc.Logghe at devgen.com (Marc Logghe)
Date: Fri, 13 Feb 2004 10:43:55 +0100
Subject: [EMBOSS] Database access external app
Message-ID: <BEE28BF86078B6429D6C780635718E210395E8@morelia.be.devgen.com>



> -----Original Message-----
> From: Stefanie Lager [mailto:stefanielager at fastmail.ca]
> Sent: vrijdag 13 februari 2004 9:53
> To: emboss at embnet.org
> Subject: RE: [EMBOSS] Database access external app
> 
> 
> Marc,
> 
> I use the same setup as you "app: "fastacmd -d hs_pub_genomic -s %s",
> and I try to retrive from a human genome database (each chr is a BIG
> fasta file). The formatdb indexing seems OK, fastacmd works on
> commandline. But I don't get any error from EMBOSS it just 
> can't retrive
> entries (it just hangs there forever). 

Hey, now you mention it ! We also have this on another machine where EMBOSS 2.8.0 is installed.
Also there it hangs when an external application should fetch the entry (from a database).
We don't have a problem on the other machines where EMBOSS 2.7.1 is installed.
So there might be an issue after all ??
Marc


From pmr at ebi.ac.uk  Fri Feb 13 09:52:02 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 13 Feb 2004 09:52:02 +0000
Subject: [EMBOSS] Database access external app
In-Reply-To: <20040213085320.4F6E7863CFF@mail.interchange.ca>
References: <20040213085320.4F6E7863CFF@mail.interchange.ca>
Message-ID: <402C9E42.1070105@ebi.ac.uk>

Stefanie Lager wrote:

> Marc,
> 
> I use the same setup as you "app: "fastacmd -d hs_pub_genomic -s %s",
> and I try to retrive from a human genome database (each chr is a BIG
> fasta file). The formatdb indexing seems OK, fastacmd works on
> commandline. But I don't get any error from EMBOSS it just can't retrive
> entries (it just hangs there forever). 

The hang is a known problem to be fixed in 2.8.1 - entries over a 
certain size will hang in 2.8.0 because we added a wait loop to catch 
zombie processes.

As a quick fix (patch version of ajfile.c to be added to the FTP 
server), you can:

edit ajax/ajfile.c

in function ajFileNewInPipe, remove this loop at the end of the function:

     ret = -1;
     while(ret != pid)
     {
         ret = wait(&status);
         if(ret == -1)
             if(ret != EINTR)
                 ret = pid;
     }

Then make (and make install if you installed EMBOSS)

This loop will hang if the external process has unread data. (The real 
fix is to move this loop to the file close functions)

Hope this helps,

Peter Rice



From stefanielager at fastmail.ca  Fri Feb 13 11:44:39 2004
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Fri, 13 Feb 2004 11:44:39 +0000 (UTC)
Subject: [EMBOSS] Database access external app
In-Reply-To: <402CA024.4060704@ebi.ac.uk>
Message-ID: <20040213114440.C6B7E861214@mail.interchange.ca>

Thank you Peter,

Changing the ajfile.c file solved the problem, and YES i do run EMBOSS
2.8.0.

Stefanie

> 
> Because the ajfile.c fix only affects sequences above a certain size,
> most protein and gene sequences in FASTA format will be too short to
> hang.
> 
> Try the ajfile.c fix ... I expect it will fix your "fastacmd problem".
> 
> If you still have problems, let me know.
> 
> regards,
> 
> Peter Rice
> 
_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians


From gbottu at ben.vub.ac.be  Fri Feb 13 20:15:46 2004
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Fri, 13 Feb 2004 21:15:46 +0100
Subject: [EMBOSS] Staden and EMBOSS 2.8.O
Message-ID: <20040213201546.GA29575@bigben.ulb.ac.be>

	Dear colleagues,

As you all know, with EMBOSS 2.8.O the syntax of the ACD files has 
changed. An unfortunate consequence is that EMBOSS programs do not work 
well or not at all anymore under Staden spin or spin2. The script 
acd2tcl.tcl should be updated as to handle new things like the rename 
required -> standard and the use of $acdprotein. Unfortunately there is no 
support for Staden anymore (well, it was recently announced that James 
Bonfield is working at Sanger Centre, but according to the Web page he is 
only developing gap4, not spin). Does someone know more about it ?

	Guy Bottu,
	BEN


From humberto at hpcf.upr.edu  Sat Feb 14 02:17:30 2004
From: humberto at hpcf.upr.edu (Humberto Ortiz Zuazaga)
Date: Fri, 13 Feb 2004 22:17:30 -0400
Subject: [EMBOSS] bioknoppix: a linux live CD with EMBOSS
Message-ID: <20040213221730.323520d7.humberto@hpcf.upr.edu>

Carlos Rodriguez and I have put together a custom KNOPPIX CD with
several bioinformatics applicacions. I'm using it to teach a
bioinformatics course at the University of Puerto Rico. The students can
take the whole course environment back to their labs, or home to
practice.

You can get the CD images from:

http://bioknoppix.hpcf.upr.edu/

The CD boots into a graphical KDE environment, with EMBOSS 2.8.0
installed, as well as ImageJ, bioconductor, R, Cn3D, rasmol, Artemis. We
also included jemboss standalone, but this release has a bug in the
jemboss installation. 

The t* databases are installed, so students can follow the tutorial or
program manual examples for EMBOSS.

This version also includes SRS access to embl, genbank, swissprot, pir
via srswww to Sanger and Indiana University.

Please download the CD images and let us know how we can improve the
system.

-- 
Humberto Ortiz-Zuazaga
Carlos Rodriguez
High Performance Computing facility
University of Puerto Rico
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From sbassi at telefax.com.ar  Sat Feb 14 03:49:15 2004
From: sbassi at telefax.com.ar (Sebastian Bassi)
Date: Sat, 14 Feb 2004 00:49:15 -0300
Subject: [EMBOSS] Linux for bioinformatics: Name change. BioShell now is DNALinux
Message-ID: <402D9ABB.5030404@telefax.com.ar>

About a month ago I posted an announce regarding Bioshell. A Linux 
distro based on a LiveCD (Slax). Thank to people at IGH and Quilmes 
National University, I put it online.
Here is the official announce:


(Quilmes, Argentina). GenesDigitales is releasing the first public 
version of a linux distribution oriented toward life science users: 
DNALinux 0.13.
     It is based on a reduced version of Slackware Linux (Slax) with 
bioinformatic software and genome data included. One key feature of 
DNALinux is that works as a LiveCD, that is, without making any 
permanent change on the hard disk. The distro could be tested or used 
without any risk of data loss. It also could be installed as a regular 
Linux if you want (check the FAQ at www.dnalinux.com for details).
     Here is the list of bioinformatics programs:

BLAST
EMBOSS-2.8.0
T-COFFEE_distribution_Version_1.37
abacus-0.63
arka-0.11
avid
big_mac
cap3
clustalx1.81.linux
e-pcr
efmc
hmmer-2.3.2.bin.intel-linux
ncbi
paml3.12
primer3_0_9_test

     Sequence data included (on BLAST format):

Arabidopsis Thaliana (aa).
Drosophila Malanogaster (aa)
Escherichia Coli (aa).

     This is a fist release, so there is a lot of things to improve. We 
are working in the next major release, set for April/May 2004. If you 
want to check this version, please take a look at www.dnalinux.com, 
where you could download DNALinux (free registration requiered).

DNALinux team at GenesDigitales: info at genesdigitales.com

                 http://Bioinformatica.info



From sbassi at telefax.com.ar  Sat Feb 14 03:58:11 2004
From: sbassi at telefax.com.ar (Sebastian Bassi)
Date: Sat, 14 Feb 2004 00:58:11 -0300
Subject: [EMBOSS] bioknoppix: a linux live CD with EMBOSS
In-Reply-To: <20040213221730.323520d7.humberto@hpcf.upr.edu>
References: <20040213221730.323520d7.humberto@hpcf.upr.edu>
Message-ID: <402D9CD3.3050509@telefax.com.ar>

Humberto Ortiz Zuazaga wrote:

> Carlos Rodriguez and I have put together a custom KNOPPIX CD with
> several bioinformatics applicacions. I'm using it to teach a
> bioinformatics course at the University of Puerto Rico. The students can
> take the whole course environment back to their labs, or home to
> practice.

Seems we are all with the same idea!.
Bioinformatics.org is hosting even another project with similar goals 
(Bio-Linux, look at http://envgen.nox.ac.uk/biolinux.html) they are 
based in RedHat but they are considering Debian/Knoppix.
I fell like making redundant work :)



From kawaji at unza.org  Sun Feb 15 16:33:39 2004
From: kawaji at unza.org (KAWAJI Hideya)
Date: Mon, 16 Feb 2004 01:33:39 +0900 (JST)
Subject: [EMBOSS] Tutorial translation into Japanese
Message-ID: <20040216.013339.907658695.kawaji@unza.org>

Hi,

We, JAMBO (Japan EMBOSS Users Group), release the translation
of the EMBOSS tutorial into Japanese. Just a section, 'Preface from translators'
(http://transgenic.cats.st/jambo/doc/tutorial_jp/node1.html)
are added, and the contributers are listed there in English and Japanese.

It is very honor if our translation is sited by the EMBOSS site,
or included by the EMBOSS package.


  [Wiki]
  http://transgenic.cats.st/jambo/index.php?%5B%5BEMBOSS%A4%F2%CD%D1%A4%A4%A4%BF%C7%DB%CE%F3%B2%F2%C0%CF%A4%D8%A4%CE%BC%EA%B0%FA%A4%AD%5D%5D

  [Archive of LaTeX source, PS ver., PDF ver.]
  http://transgenic.cats.st/jambo/doc/tutorial_jp/emboss_tutorial_ja.Release1.zip

  [HTML ver.]
  http://transgenic.cats.st/jambo/doc/tutorial_jp/index.html

  [Archive of HTML ver.]
http://transgenic.cats.st/jambo/doc/tutorial_jp/emboss_tutorial_ja_html.Release1.zip

  [PDF ver.]
  http://transgenic.cats.st/jambo/doc/tutorial_jp/emboss_tutorial_ja.pdf


Best regards,
---
Hideya KAWAJI <kawaji at unza.org>  # My e-mail address has been changed


From simon.andrews at bbsrc.ac.uk  Mon Feb 16 08:19:33 2004
From: simon.andrews at bbsrc.ac.uk (simon andrews (BI))
Date: Mon, 16 Feb 2004 08:19:33 -0000
Subject: [EMBOSS] Staden and EMBOSS 2.8.O
Message-ID: <2DC41140A89ED411989D00508BDCD9ED01E28CD0@bi-exsrv1.iapc.bbsrc.ac.uk>



> -----Original Message-----
> From: Guy Bottu [mailto:gbottu at ben.vub.ac.be] 
> Subject: [EMBOSS] Staden and EMBOSS 2.8.O
> 
> Unfortunately there is no support for Staden anymore (well, 
> it was recently announced that James Bonfield is working 
> at Sanger Centre, but according to the Web page he is 
> only developing gap4, not spin). Does someone know more about it ?

James recently announced that the MRC have finally agreed to release Staden under an opensource licence.  It is therefore now being hosted and developed as a sourceforge project:

http://staden.sourceforge.net/

https://sourceforge.net/projects/staden

..therefore if you're up to making the changes yourself you can submit patches to the project, or if not you can file it as a bug which someone else will hopefully pick up.

Simon.


From kawaji at unza.org  Mon Feb 16 14:48:49 2004
From: kawaji at unza.org (KAWAJI Hideya)
Date: Mon, 16 Feb 2004 23:48:49 +0900 (JST)
Subject: [EMBOSS] Re: Tutorial translation into Japanese
In-Reply-To: <20040216.013339.907658695.kawaji@unza.org>
References: <20040216.013339.907658695.kawaji@unza.org>
Message-ID: <20040216.234849.373533604.kawaji@unza.org>

Hi, 


In my translation into Japanese, I found just a small point to be corrected
in the EMBOSS tutorial.

It's in the chapter 'Working with sequences'. 
http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Doc/Tutorial/emboss_tutorial/node2.html

Although 'seqretallfeat' is mentioned to retrieve all features,
it has been integrated into 'seqret', due to version up.
It should be replaced by 'seqret -feature' for current version.

best,
---
Hideya KAWAJI <kawaji at unza.org>


From m.claesson at student.ucc.ie  Tue Feb 17 10:58:29 2004
From: m.claesson at student.ucc.ie (Marcus Claesson)
Date: 17 Feb 2004 10:58:29 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
Message-ID: <1077015509.5582.15.camel@morpheus.ucc.ie>

Hello,

I have a silly little problem indexing databases in Emboss-2.8.0. After
running dbifasta and adding DB entries in emboss.default I can only
access the database when being in the same directory as the fasta file.
Here is what I did:

[blast_db]$ uname -a
Linux neo.ucc.ie 2.4.9-e.35enterprise #1 SMP Tue Dec 23 00:06:16 EST
2003 i686 unknown

[blast_db]$ pwd
/var/data/blast_db

[blast_db]$ ll ecoli.nt
-rw-r--r--    1 marcus   bioinfo   4763013 Jan 15 01:38 ecoli.nt

[blast_db]$ dbifasta
Index a fasta database
    simple : >ID
     idacc : >ID ACC
     gcgid : >db:ID
  gcgidacc : >db:ID ACC
      dbid : >db ID
      ncbi : | formats
ID line format [idacc]: 
Database directory [.]: /var/data/blast_db
Wildcard database filename [*.dat]: ecoli.nt
Database name: ecoli.nt
Release number [0.0]: 
Index date [00/00/00]:

[blast_db]$ ll entrynam.idx division.lkp acnum.*
-rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 acnum.hit
-rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 acnum.trg
-rw-rw-r--    1 marcus   bioinfo       330 Feb 17 10:39 division.lkp
-rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 entrynam.idx

Added these lines in /usr/local/EMBOSS-2.8.0/emboss/emboss.default:

DB ecoli.nt [
   type: "N"
   format: "fasta"
   method: "emblcd"
   dir: "/var/data/blast_db/"
]

[blast_db]$ showdb
Displays information on the currently available databases
# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
ecoli.nt      N    OK  OK  OK  -

[blast_db]$ cd ~

[marcus]$ seqret ecoli.nt
Reads and writes (returns) sequences
Error: failed to open filename 'ecoli.nt'
Error: Unable to read sequence 'ecoli.nt'
Died: seqret terminated: Bad value for '-sequence' and no prompt

But it works when I'm the same directory as ecoli.nt:

[blast_db]$  seqret ecoli.nt
Reads and writes (returns) sequences
Output sequence [ae000111.fasta]: 
etc...

Clearly it must be possible to access ecoli.nt from other directories?


Extremly grateful for any help on this!

Regards,
Marcus





From MAILER-DAEMON at pool.informatik.rwth-aachen.de  Tue Feb 17 13:33:48 2004
From: MAILER-DAEMON at pool.informatik.rwth-aachen.de (Mail Delivery System)
Date: Tue, 17 Feb 2004 14:33:48 +0100 (CET)
Subject: [EMBOSS] Undelivered Mail Returned to Sender
Message-ID: <20040217133348.3573AA8CF@poolmail.informatik.rwth-aachen.de>

This is the Postfix program at host poolmail.informatik.rwth-aachen.de.

I'm sorry to have to inform you that the message returned
below could not be delivered to one or more destinations.

For further assistance, please send mail to <postmaster>

If you do so, please include this problem report. You can
delete your own text from the message returned below.

			The Postfix program

<maria at pool.informatik.rwth-aachen.de>: unknown user: "maria"
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From jlaroche at bioinfo.ulaval.ca  Tue Feb 17 13:57:51 2004
From: jlaroche at bioinfo.ulaval.ca (=?ISO-8859-1?Q?J=E9r=F4me_Laroche?=)
Date: Tue, 17 Feb 2004 08:57:51 -0500
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <1077015509.5582.15.camel@morpheus.ucc.ie>
References: <1077015509.5582.15.camel@morpheus.ucc.ie>
Message-ID: <46996444-6151-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>

Hi Marcus,

  it seems that your file .emboss_default don't have the line to specify 
the location of the indexed database (check the last line of my 
example).
Also, you can add this line at the begining of your file (setting a 
variable for the path of your database) so if you move your database 
and your index, you just have to modify the path at this line.



SET jerome_database_dir /cbi/people/jlaroche/data/banquesemboss


DB rbcl [
    type: N
    method: emblcd
    format: fasta
    dir: $jerome_database_dir/banque1
    indexdir: $jerome_database_dir/banque1
]



Jerome

Centre de bioinformatique
Pavillon Charles-Eug?ne-Marchand
Bureau 4233d
t?l: 418-656-2131 poste 6184
fax: 418-656-7176
www.bioinfo.ulaval.ca


Le 04-02-17, ? 05:58, Marcus Claesson a ?crit :

> Hello,
>
> I have a silly little problem indexing databases in Emboss-2.8.0. After
> running dbifasta and adding DB entries in emboss.default I can only
> access the database when being in the same directory as the fasta file.
> Here is what I did:
>
> [blast_db]$ uname -a
> Linux neo.ucc.ie 2.4.9-e.35enterprise #1 SMP Tue Dec 23 00:06:16 EST
> 2003 i686 unknown
>
> [blast_db]$ pwd
> /var/data/blast_db
>
> [blast_db]$ ll ecoli.nt
> -rw-r--r--    1 marcus   bioinfo   4763013 Jan 15 01:38 ecoli.nt
>
> [blast_db]$ dbifasta
> Index a fasta database
>     simple : >ID
>      idacc : >ID ACC
>      gcgid : >db:ID
>   gcgidacc : >db:ID ACC
>       dbid : >db ID
>       ncbi : | formats
> ID line format [idacc]:
> Database directory [.]: /var/data/blast_db
> Wildcard database filename [*.dat]: ecoli.nt
> Database name: ecoli.nt
> Release number [0.0]:
> Index date [00/00/00]:
>
> [blast_db]$ ll entrynam.idx division.lkp acnum.*
> -rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 acnum.hit
> -rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 acnum.trg
> -rw-rw-r--    1 marcus   bioinfo       330 Feb 17 10:39 division.lkp
> -rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 entrynam.idx
>
> Added these lines in /usr/local/EMBOSS-2.8.0/emboss/emboss.default:
>
> DB ecoli.nt [
>    type: "N"
>    format: "fasta"
>    method: "emblcd"
>    dir: "/var/data/blast_db/"
> ]
>
> [blast_db]$ showdb
> Displays information on the currently available databases
> # Name        Type ID  Qry All Comment
> # ====        ==== ==  === === =======
> ecoli.nt      N    OK  OK  OK  -
>
> [blast_db]$ cd ~
>
> [marcus]$ seqret ecoli.nt
> Reads and writes (returns) sequences
> Error: failed to open filename 'ecoli.nt'
> Error: Unable to read sequence 'ecoli.nt'
> Died: seqret terminated: Bad value for '-sequence' and no prompt
>
> But it works when I'm the same directory as ecoli.nt:
>
> [blast_db]$  seqret ecoli.nt
> Reads and writes (returns) sequences
> Output sequence [ae000111.fasta]:
> etc...
>
> Clearly it must be possible to access ecoli.nt from other directories?
>
>
> Extremly grateful for any help on this!
>
> Regards,
> Marcus
>
>



From m.claesson at student.ucc.ie  Tue Feb 17 14:49:47 2004
From: m.claesson at student.ucc.ie (Marcus Claesson)
Date: 17 Feb 2004 14:49:47 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <46996444-6151-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
References: <1077015509.5582.15.camel@morpheus.ucc.ie>
	 <46996444-6151-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
Message-ID: <1077029387.5582.24.camel@morpheus.ucc.ie>

Thanks for your answer Jerome! But it didn't seem to help me. I added
the indexdir line with the same path (where the index files and fasta
file is) as "dir:". I tried this both with and without setting a
emboss_db_dir variable, but it still didn't work. In other words I can
still only access the database (that shows up in showdb) if I am in that
fasta file directory.

Do I need to set this path somewhere else than in emboss.default you
think?

Marcus



On Tue, 2004-02-17 at 13:57, J?r?me Laroche wrote:
> Hi Marcus,
> 
>   it seems that your file .emboss_default don't have the line to specify 
> the location of the indexed database (check the last line of my 
> example).
> Also, you can add this line at the begining of your file (setting a 
> variable for the path of your database) so if you move your database 
> and your index, you just have to modify the path at this line.
> 
> 
> 
> SET jerome_database_dir /cbi/people/jlaroche/data/banquesemboss
> 
> 
> DB rbcl [
>     type: N
>     method: emblcd
>     format: fasta
>     dir: $jerome_database_dir/banque1
>     indexdir: $jerome_database_dir/banque1
> ]
> 
> 
> 
> Jerome
> 
> Centre de bioinformatique
> Pavillon Charles-Eug?ne-Marchand
> Bureau 4233d
> t?l: 418-656-2131 poste 6184
> fax: 418-656-7176
> www.bioinfo.ulaval.ca
> 
> 
> Le 04-02-17, ? 05:58, Marcus Claesson a ?crit :
> 
> > Hello,
> >
> > I have a silly little problem indexing databases in Emboss-2.8.0. After
> > running dbifasta and adding DB entries in emboss.default I can only
> > access the database when being in the same directory as the fasta file.
> > Here is what I did:
> >
> > [blast_db]$ uname -a
> > Linux neo.ucc.ie 2.4.9-e.35enterprise #1 SMP Tue Dec 23 00:06:16 EST
> > 2003 i686 unknown
> >
> > [blast_db]$ pwd
> > /var/data/blast_db
> >
> > [blast_db]$ ll ecoli.nt
> > -rw-r--r--    1 marcus   bioinfo   4763013 Jan 15 01:38 ecoli.nt
> >
> > [blast_db]$ dbifasta
> > Index a fasta database
> >     simple : >ID
> >      idacc : >ID ACC
> >      gcgid : >db:ID
> >   gcgidacc : >db:ID ACC
> >       dbid : >db ID
> >       ncbi : | formats
> > ID line format [idacc]:
> > Database directory [.]: /var/data/blast_db
> > Wildcard database filename [*.dat]: ecoli.nt
> > Database name: ecoli.nt
> > Release number [0.0]:
> > Index date [00/00/00]:
> >
> > [blast_db]$ ll entrynam.idx division.lkp acnum.*
> > -rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 acnum.hit
> > -rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 acnum.trg
> > -rw-rw-r--    1 marcus   bioinfo       330 Feb 17 10:39 division.lkp
> > -rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 entrynam.idx
> >
> > Added these lines in /usr/local/EMBOSS-2.8.0/emboss/emboss.default:
> >
> > DB ecoli.nt [
> >    type: "N"
> >    format: "fasta"
> >    method: "emblcd"
> >    dir: "/var/data/blast_db/"
> > ]
> >
> > [blast_db]$ showdb
> > Displays information on the currently available databases
> > # Name        Type ID  Qry All Comment
> > # ====        ==== ==  === === =======
> > ecoli.nt      N    OK  OK  OK  -
> >
> > [blast_db]$ cd ~
> >
> > [marcus]$ seqret ecoli.nt
> > Reads and writes (returns) sequences
> > Error: failed to open filename 'ecoli.nt'
> > Error: Unable to read sequence 'ecoli.nt'
> > Died: seqret terminated: Bad value for '-sequence' and no prompt
> >
> > But it works when I'm the same directory as ecoli.nt:
> >
> > [blast_db]$  seqret ecoli.nt
> > Reads and writes (returns) sequences
> > Output sequence [ae000111.fasta]:
> > etc...
> >
> > Clearly it must be possible to access ecoli.nt from other directories?
> >
> >
> > Extremly grateful for any help on this!
> >
> > Regards,
> > Marcus
> >
> >
> 



From m.claesson at student.ucc.ie  Tue Feb 17 15:23:32 2004
From: m.claesson at student.ucc.ie (Marcus Claesson)
Date: 17 Feb 2004 15:23:32 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <BC57DECC.DA37%d.m.a.martin@dundee.ac.uk>
References: <BC57DECC.DA37%d.m.a.martin@dundee.ac.uk>
Message-ID: <1077031412.5582.32.camel@morpheus.ucc.ie>

Hi,

I have now changed emboss/emboss.defaults to:

SET $emboss_db_dir /var/data/blast_db

DB ecoli.nt [
   type: "N"
   format: "fasta"
   method: "emblcd"
   dir: "$emboss_db_dir"
   indexdir: "$emboss_db_dir"
   file: "ecoli.nt"
]

And get the same negative result:

[marcus]$ showdb
Displays information on the currently available databases
# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
ecoli.nt      N    OK  OK  OK  -

[marcus]$ seqret ecoli.nt
Reads and writes (returns) sequences
Error: failed to open filename 'ecoli.nt'
Error: Unable to read sequence 'ecoli.nt'
Died: seqret terminated: Bad value for '-sequence' and no prompt

I find this very strange! If you don't know what's wrong would you know
anywhere else I can get help with this?

Thanks again.

Marcus


On Tue, 2004-02-17 at 15:07, David Martin wrote:
> On 17/2/04 2:49 pm, "Marcus Claesson" <m.claesson at student.ucc.ie> wrote:
> 
> > Thanks for your answer Jerome! But it didn't seem to help me. I added
> > the indexdir line with the same path (where the index files and fasta
> > file is) as "dir:". I tried this both with and without setting a
> > emboss_db_dir variable, but it still didn't work. In other words I can
> > still only access the database (that shows up in showdb) if I am in that
> > fasta file directory.
> 
> This is because you have not set the file: option? try that and see if it
> works.
> in the original example you give the database the same name as the fasta
> file so it works if it is in the right directory.
> 
> > 
> > Do I need to set this path somewhere else than in emboss.default you
> > think?
> 
> >> SET jerome_database_dir /cbi/people/jlaroche/data/banquesemboss
> >> 
> >> 
> >> DB rbcl [
> >>     type: N
> >>     method: emblcd
> >>     format: fasta
> >>     dir: $jerome_database_dir/banque1
> >>     indexdir: $jerome_database_dir/banque1
>        file: seqfile.fasta
>        comment: "It is useful to put a description here"
> >> ]
> 
> 
> ..d



From d.m.a.martin at dundee.ac.uk  Tue Feb 17 15:28:42 2004
From: d.m.a.martin at dundee.ac.uk (David Martin)
Date: Tue, 17 Feb 2004 15:28:42 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <1077031412.5582.32.camel@morpheus.ucc.ie>
Message-ID: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk>

On 17/2/04 3:23 pm, "Marcus Claesson" <m.claesson at student.ucc.ie> wrote:

> Hi,
> 
> I have now changed emboss/emboss.defaults to:
> 
> SET $emboss_db_dir /var/data/blast_db
> 
> DB ecoli.nt [
>  type: "N"
>  format: "fasta"
>  method: "emblcd"
>  dir: "$emboss_db_dir"
>  indexdir: "$emboss_db_dir"
>  file: "ecoli.nt"
> ]
> 
> And get the same negative result:
> 
> [marcus]$ showdb
> Displays information on the currently available databases
> # Name        Type ID  Qry All Comment
> # ====        ==== ==  === === =======
> ecoli.nt      N    OK  OK  OK  -
> 
> [marcus]$ seqret ecoli.nt

'seqret ecoli.nt:\*' perhaps?

..d

> Reads and writes (returns) sequences
> Error: failed to open filename 'ecoli.nt'
> Error: Unable to read sequence 'ecoli.nt'
> Died: seqret terminated: Bad value for '-sequence' and no prompt
> 
> I find this very strange! If you don't know what's wrong would you know
> anywhere else I can get help with this?
> 
> Thanks again.
> 
> Marcus
> 
> 
> On Tue, 2004-02-17 at 15:07, David Martin wrote:
>> On 17/2/04 2:49 pm, "Marcus Claesson" <m.claesson at student.ucc.ie> wrote:
>> 
>>> Thanks for your answer Jerome! But it didn't seem to help me. I added
>>> the indexdir line with the same path (where the index files and fasta
>>> file is) as "dir:". I tried this both with and without setting a
>>> emboss_db_dir variable, but it still didn't work. In other words I can
>>> still only access the database (that shows up in showdb) if I am in that
>>> fasta file directory.
>> 
>> This is because you have not set the file: option? try that and see if it
>> works.
>> in the original example you give the database the same name as the fasta
>> file so it works if it is in the right directory.
>> 
>>> 
>>> Do I need to set this path somewhere else than in emboss.default you
>>> think?
>> 
>>>> SET jerome_database_dir /cbi/people/jlaroche/data/banquesemboss
>>>> 
>>>> 
>>>> DB rbcl [
>>>>     type: N
>>>>     method: emblcd
>>>>     format: fasta
>>>>     dir: $jerome_database_dir/banque1
>>>>     indexdir: $jerome_database_dir/banque1
>>        file: seqfile.fasta
>>        comment: "It is useful to put a description here"
>>>> ]
>> 
>> 
>> ..d
> 
> 



From gwilliam at hgmp.mrc.ac.uk  Tue Feb 17 15:31:08 2004
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Tue, 17 Feb 2004 15:31:08 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
References: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk>
Message-ID: <403233BC.BD3BF7C4@hgmp.mrc.ac.uk>

David Martin wrote:
> 
> On 17/2/04 3:23 pm, "Marcus Claesson" <m.claesson at student.ucc.ie> wrote:
> 
> > Hi,
> >
> > I have now changed emboss/emboss.defaults to:
> >
> > SET $emboss_db_dir /var/data/blast_db
> >
> > DB ecoli.nt [
> >  type: "N"
> >  format: "fasta"
> >  method: "emblcd"
> >  dir: "$emboss_db_dir"
> >  indexdir: "$emboss_db_dir"
> >  file: "ecoli.nt"
> > ]
> >
> > And get the same negative result:
> >
> > [marcus]$ showdb
> > Displays information on the currently available databases
> > # Name        Type ID  Qry All Comment
> > # ====        ==== ==  === === =======
> > ecoli.nt      N    OK  OK  OK  -
> >
> > [marcus]$ seqret ecoli.nt
> 
> 'seqret ecoli.nt:\*' perhaps?

That would be more explicit and clearer for other people to read, but a
database-name on its own is a perfectly legal EMBOSS USA.

Try: 'seqret embl'

-- 
Gary Williams
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494522			Fax: +44 1223 494512
E-mail: gwilliam at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk


From Marc.Logghe at devgen.com  Tue Feb 17 15:32:10 2004
From: Marc.Logghe at devgen.com (Marc Logghe)
Date: Tue, 17 Feb 2004 16:32:10 +0100
Subject: [EMBOSS] can't access databases indexed by dbifasta
Message-ID: <BEE28BF86078B6429D6C780635718E21904B9A@morelia.be.devgen.com>

Hi,
Reminds me of a problem I had a while ago. Maybe it is a similar problem. Have a look at: http://www.hgmp.mrc.ac.uk/Emboss/HYPERMAIL/emboss/emboss.200305/0008.html
HTH,
Marc

> -----Original Message-----
> From: Marcus Claesson [mailto:m.claesson at student.ucc.ie]
> Sent: dinsdag 17 februari 2004 16:24
> To: David Martin
> Cc: emboss at embnet.org
> Subject: Re: [EMBOSS] can't access databases indexed by dbifasta
> 
> 
> Hi,
> 
> I have now changed emboss/emboss.defaults to:
> 
> SET $emboss_db_dir /var/data/blast_db
> 
> DB ecoli.nt [
>    type: "N"
>    format: "fasta"
>    method: "emblcd"
>    dir: "$emboss_db_dir"
>    indexdir: "$emboss_db_dir"
>    file: "ecoli.nt"
> ]
> 
> And get the same negative result:
> 
> [marcus]$ showdb
> Displays information on the currently available databases
> # Name        Type ID  Qry All Comment
> # ====        ==== ==  === === =======
> ecoli.nt      N    OK  OK  OK  -
> 
> [marcus]$ seqret ecoli.nt
> Reads and writes (returns) sequences
> Error: failed to open filename 'ecoli.nt'
> Error: Unable to read sequence 'ecoli.nt'
> Died: seqret terminated: Bad value for '-sequence' and no prompt
> 
> I find this very strange! If you don't know what's wrong 
> would you know
> anywhere else I can get help with this?
> 
> Thanks again.
> 
> Marcus
> 
> 
> On Tue, 2004-02-17 at 15:07, David Martin wrote:
> > On 17/2/04 2:49 pm, "Marcus Claesson" 
> <m.claesson at student.ucc.ie> wrote:
> > 
> > > Thanks for your answer Jerome! But it didn't seem to help 
> me. I added
> > > the indexdir line with the same path (where the index 
> files and fasta
> > > file is) as "dir:". I tried this both with and without setting a
> > > emboss_db_dir variable, but it still didn't work. In 
> other words I can
> > > still only access the database (that shows up in showdb) 
> if I am in that
> > > fasta file directory.
> > 
> > This is because you have not set the file: option? try that 
> and see if it
> > works.
> > in the original example you give the database the same name 
> as the fasta
> > file so it works if it is in the right directory.
> > 
> > > 
> > > Do I need to set this path somewhere else than in 
> emboss.default you
> > > think?
> > 
> > >> SET jerome_database_dir /cbi/people/jlaroche/data/banquesemboss
> > >> 
> > >> 
> > >> DB rbcl [
> > >>     type: N
> > >>     method: emblcd
> > >>     format: fasta
> > >>     dir: $jerome_database_dir/banque1
> > >>     indexdir: $jerome_database_dir/banque1
> >        file: seqfile.fasta
> >        comment: "It is useful to put a description here"
> > >> ]
> > 
> > 
> > ..d
> 
> 


From m.claesson at student.ucc.ie  Tue Feb 17 15:41:02 2004
From: m.claesson at student.ucc.ie (Marcus Claesson)
Date: 17 Feb 2004 15:41:02 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk>
References: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk>
Message-ID: <1077032461.5582.34.camel@morpheus.ucc.ie>


> 'seqret ecoli.nt:\*' perhaps?

Nope, same bad result...

/M



From jlaroche at bioinfo.ulaval.ca  Tue Feb 17 15:50:16 2004
From: jlaroche at bioinfo.ulaval.ca (=?ISO-8859-1?Q?J=E9r=F4me_Laroche?=)
Date: Tue, 17 Feb 2004 10:50:16 -0500
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <1077032461.5582.34.camel@morpheus.ucc.ie>
References: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk> <1077032461.5582.34.camel@morpheus.ucc.ie>
Message-ID: <FB53EFC8-6160-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>

Marcus,

as suggested earlier by David, take a different name for your database. 
Take only ecoli or something else. I try this with my data and I got 
the same problem.


Jerome

Centre de bioinformatique
Pavillon Charles-Eug?ne-Marchand
Bureau 4233d
t?l: 418-656-2131 poste 6184
fax: 418-656-7176
www.bioinfo.ulaval.ca
Le 04-02-17, ? 10:41, Marcus Claesson a ?crit :

>
>> 'seqret ecoli.nt:\*' perhaps?
>
> Nope, same bad result...
>
> /M
>



From m.claesson at student.ucc.ie  Wed Feb 18 13:40:43 2004
From: m.claesson at student.ucc.ie (Marcus Claesson)
Date: 18 Feb 2004 13:40:43 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <11B65834-6169-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
References: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk>
	 <1077032461.5582.34.camel@morpheus.ucc.ie>
	 <FB53EFC8-6160-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
	 <1077035334.5582.38.camel@morpheus.ucc.ie>
	 <11B65834-6169-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
Message-ID: <1077111643.25361.59.camel@morpheus.ucc.ie>

I entered a 'field' in both dbifasta and emboss.defaults and it works
now! This is what I did (I have one last tiny question in the end):

[blast_db]$ dbifasta -fields des
Index a fasta database
    simple : >ID
     idacc : >ID ACC
     gcgid : >db:ID
  gcgidacc : >db:ID ACC
      dbid : >db ID
      ncbi : | formats
ID line format [idacc]: ncbi
Database directory [.]: 
Wildcard database filename [*.dat]: ecoli.nt
Database name: ecoli_nt
Release number [0.0]: 
Index date [00/00/00]:

in emboss/emboss.defaults:
DB ecoli_nt [
   type: N
   format: fasta
   method: emblcd
   dir: 
   indexdir: 
   file: ecoli.nt
   fields: des
]

[blast_db]$ showdb
Displays information on the currently available databases
# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
ecoli_nt      N    OK  OK  OK  -


Now this works:
[marcus]$ seqret ecoli_nt:NC_0012\*
>NC_001224.1 NC_001224.1 Saccharomyces cerevisiae mitochondrion,
complete genome
TTCATAATTAATTTTTTATATATATATTATATTATAATATTAATTTATATTATAAAAATA
ATATTTATTATTAAAATATTTATTCTCCTTTCGGGGTTCCGGCTCCCGTGGCCGGGCCCC
GGAATTATTAATTAATAATAAATTATTATTAATAATTATTTATTATTTTAT


But this doesn't work and I don't know why since I added the 'des
field'. Are queries like these suppose to work by the way?

[marcus]$ seqret ecoli_nt:\*mitochondrio\* -auto -stdout
Error: Unable to read sequence 'ecoli_nt:*mitochondrio*'
Died: seqret terminated: Bad value for '-sequence' with -auto defined


Thanks for all help so far!

Marcus






On Tue, 2004-02-17 at 16:48, J?r?me Laroche wrote:
> Marcus,
> 
> which one is the right? Because in the first, at the question "Wildcard 
> database filename:" you enter only ecoli and I think that your sequence 
> file is ecoli.nt It is only at the line "Database name:" that you enter 
> the name ecoli (without the nt). If it doesn't work, check again your 
> emboss_default file and ensure you have the requested field for your 
> database and your index and the right syntax for the location of your 
> file.
> 
> Finally, reply to all, for all the people know what is the right thing 
> to do in that case.
> 
> 
> Good luck!
> 
> Jerome
> 
> 
> > This is how I created it:
> > [blast_db]$ dbifasta
> > Index a fasta database
> >     simple : >ID
> >      idacc : >ID ACC
> >      gcgid : >db:ID
> >   gcgidacc : >db:ID ACC
> >       dbid : >db ID
> >       ncbi : | formats
> > ID line format [idacc]:
> > Database directory [.]: /var/data/blast_db
> > Wildcard database filename [*.dat]: ecoli
> > Database name: ecoli
> >
> 
> > [marcus at neo blast_db]$ dbifasta
> > Index a fasta database
> >     simple : >ID
> >      idacc : >ID ACC
> >      gcgid : >db:ID
> >   gcgidacc : >db:ID ACC
> >       dbid : >db ID
> >       ncbi : | formats
> > ID line format [idacc]:
> > Database directory [.]: /var/data/blast_db
> > Wildcard database filename [*.dat]: ecoli.nt
> > Database name: ecoli
> > Release number [0.0]:
> > Index date [00/00/00]:
> 
> 
> 
> Jerome
> 
> Centre de bioinformatique
> Pavillon Charles-Eug?ne-Marchand
> Bureau 4233d
> t?l: 418-656-2131 poste 6184
> fax: 418-656-7176
> www.bioinfo.ulaval.ca
> Le 04-02-17, ? 11:29, Marcus Claesson a ?crit :
> 
> > Thanks Jerome it works! However there is one thing I don't understand
> > (or I just misunderstood the syntax)...
> >
> > This happens when I want a certain entry from this new ecoli db:
> >
> > [marcus]$ seqret ecoli:AE00011\* -stdout -auto
> > Error: Unable to read sequence 'ecoli:AE00011*'
> > Died: seqret terminated: Bad value for '-sequence' with -auto defined
> >
> > The entry looks like:
> > [marcus]$ seqret ecoli -stdout -auto |head
> >> AE000111 AE000111.1 Escherichia coli K-12 MG1655 section 1 of 400 of
> > the complete geno
> > me
> > AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
> > TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTT
> >
> >
> > This is how I created it:
> > [blast_db]$ dbifasta
> > Index a fasta database
> >     simple : >ID
> >      idacc : >ID ACC
> >      gcgid : >db:ID
> >   gcgidacc : >db:ID ACC
> >       dbid : >db ID
> >       ncbi : | formats
> > ID line format [idacc]:
> > Database directory [.]: /var/data/blast_db
> > Wildcard database filename [*.dat]: ecoli
> > Database name: ecoli
> > [marcus at neo blast_db]$ dbifasta
> > Index a fasta database
> >     simple : >ID
> >      idacc : >ID ACC
> >      gcgid : >db:ID
> >   gcgidacc : >db:ID ACC
> >       dbid : >db ID
> >       ncbi : | formats
> > ID line format [idacc]:
> > Database directory [.]: /var/data/blast_db
> > Wildcard database filename [*.dat]: ecoli.nt
> > Database name: ecoli
> > Release number [0.0]:
> > Index date [00/00/00]:
> >
> >
> > Thanks again!
> > Marcus
> >
> >
> > On Tue, 2004-02-17 at 15:50, J?r?me Laroche wrote:
> >> Marcus,
> >>
> >> as suggested earlier by David, take a different name for your 
> >> database.
> >> Take only ecoli or something else. I try this with my data and I got
> >> the same problem.
> >>
> >>
> >> Jerome
> >>
> >> Centre de bioinformatique
> >> Pavillon Charles-Eug?ne-Marchand
> >> Bureau 4233d
> >> t?l: 418-656-2131 poste 6184
> >> fax: 418-656-7176
> >> www.bioinfo.ulaval.ca
> >> Le 04-02-17, ? 10:41, Marcus Claesson a ?crit :
> >>
> >>>
> >>>> 'seqret ecoli.nt:\*' perhaps?
> >>>
> >>> Nope, same bad result...
> >>>
> >>> /M
> >>>
> >>
> >
> 



From gwilliam at hgmp.mrc.ac.uk  Wed Feb 18 13:47:31 2004
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Wed, 18 Feb 2004 13:47:31 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
References: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk>
		 <1077032461.5582.34.camel@morpheus.ucc.ie>
		 <FB53EFC8-6160-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
		 <1077035334.5582.38.camel@morpheus.ucc.ie>
		 <11B65834-6169-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca> <1077111643.25361.59.camel@morpheus.ucc.ie>
Message-ID: <40336CF3.18E39E7C@hgmp.mrc.ac.uk>

Marcus Claesson wrote:
> But this doesn't work and I don't know why since I added the 'des
> field'. Are queries like these suppose to work by the way?
> 
> [marcus]$ seqret ecoli_nt:\*mitochondrio\* -auto -stdout
> Error: Unable to read sequence 'ecoli_nt:*mitochondrio*'
> Died: seqret terminated: Bad value for '-sequence' with -auto defined

The correct syntax should be:
seqret ecoli_nt-des:\*mitochondrio\* -auto -stdout
See:
http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Themes/UniformSequenceAddress.html#keys

-- 
Gary Williams
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494522			Fax: +44 1223 494512
E-mail: gwilliam at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk


From m.claesson at student.ucc.ie  Wed Feb 18 14:52:08 2004
From: m.claesson at student.ucc.ie (Marcus Claesson)
Date: 18 Feb 2004 14:52:08 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <40336D9C.1E5D2AF4@hgmp.mrc.ac.uk>
References: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk>
	 <1077032461.5582.34.camel@morpheus.ucc.ie>
	 <FB53EFC8-6160-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
	 <1077035334.5582.38.camel@morpheus.ucc.ie>
	 <11B65834-6169-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
	 <1077111643.25361.59.camel@morpheus.ucc.ie>
	 <40336CF3.18E39E7C@hgmp.mrc.ac.uk>  <40336D9C.1E5D2AF4@hgmp.mrc.ac.uk>
Message-ID: <1077115928.25361.94.camel@morpheus.ucc.ie>

That works fine now, thanks!

But I continue struggling with upcoming problems and you must be tired
of me asking questions all the time... (It's either me or the emboss man
pages that are bad, probably a mix ;))

Anyway, when I want to create a second database ecoli_aa, dbifasta seems
to overwrite the old indexfiles.

This works all fine:

[marcus]$ dbifasta -idformat ncbi -directory /var/data/blast_db
-filenames ecoli.nt -fields des -dbname ecoli_nt -release 0.0 -date
00/00/00
[marcus]$ seqret ecoli_nt: -auto -stdout|head
>AE000111 AE000111.1 Escherichia coli K-12 MG1655 section 1 of 400 of
the complete genome
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
ACAA

I add a second database: 

[marcus]$ dbifasta -idformat ncbi -directory /var/data/blast_db
-filenames ecoli.aa -fields des -dbname ecoli_aa -release 0.0 -date
00/00/00

And when I seqret the old ecoli_nt I get the new ecoli_aa entries
instead:

[marcus]$ seqret ecoli_nt: -auto -stdout|head
>AAC73112.1 (AE000111) thr operon leader peptide [Escherichia coli]
MKRISTTITTTITITTGNGAG
>AAC73113.1 (AE000111) aspartokinase I, homoserine dehydrogenase I
[Escherichia coli]
MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA
LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA
ALICRGEKMSIAIMAGV


I tried to run dbifasta for both fasta files at the same time but it
didn't work:
dbifasta -idformat ncbi -directory /var/data/blast_db -filenames
ecoli.nt ecoli.aa -fields des -dbname ecoli_nt ecoli_aa -release 0.0
-date 00/00/00

How can new databases be added without overwriting the old indexfiles?


/Marcus




On Wed, 2004-02-18 at 13:50, Gary Williams, Tel 01223 494522 wrote:
> "Gary Williams, Tel 01223 494522" wrote:
> > 
> > Marcus Claesson wrote:
> > > But this doesn't work and I don't know why since I added the 'des
> > > field'. Are queries like these suppose to work by the way?
> > >
> > > [marcus]$ seqret ecoli_nt:\*mitochondrio\* -auto -stdout
> > > Error: Unable to read sequence 'ecoli_nt:*mitochondrio*'
> > > Died: seqret terminated: Bad value for '-sequence' with -auto defined
> > 
> > The correct syntax should be:
> > seqret ecoli_nt-des:\*mitochondrio\* -auto -stdout
> > See:
> > http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Themes/UniformSequenceAddress.html#keys
> 
> I think that the '*' are not required, so:
> seqret ecoli_nt-des:mitochondrio -auto -stdout



From jlaroche at bioinfo.ulaval.ca  Wed Feb 18 15:02:33 2004
From: jlaroche at bioinfo.ulaval.ca (=?ISO-8859-1?Q?J=E9r=F4me_Laroche?=)
Date: Wed, 18 Feb 2004 10:02:33 -0500
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <1077115928.25361.94.camel@morpheus.ucc.ie>
References: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk> <1077032461.5582.34.camel@morpheus.ucc.ie> <FB53EFC8-6160-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca> <1077035334.5582.38.camel@morpheus.ucc.ie> <11B65834-6169-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca> <1077111643.25361.59.camel@morpheus.ucc.ie> <40336CF3.18E39E7C@hgmp.mrc.ac.uk>  <40336D9C.1E5D2AF4@hgmp.mrc.ac.uk> <1077115928.25361.94.camel@morpheus.ucc.ie>
Message-ID: <7AFB6596-6223-11D8-A3F2-000A95CDA6C0@bioinfo.ulaval.ca>

Marcus,

yes, the indexed files will always have the same names (I think this is  
in the EMBOSS administrator's guide):

acnum.hit  acnum.trg  division.lkp  entrynam.idx

That's why you must put these files in different directories. The  
sequence files could be in the same directory.


Jerome

Centre de bioinformatique
Pavillon Charles-Eug?ne-Marchand
Bureau 4233d
t?l: 418-656-2131 poste 6184
fax: 418-656-7176
www.bioinfo.ulaval.ca
Le 04-02-18, ? 09:52, Marcus Claesson a ?crit :

> That works fine now, thanks!
>
> But I continue struggling with upcoming problems and you must be tired
> of me asking questions all the time... (It's either me or the emboss  
> man
> pages that are bad, probably a mix ;))
>
> Anyway, when I want to create a second database ecoli_aa, dbifasta  
> seems
> to overwrite the old indexfiles.
>
> This works all fine:
>
> [marcus]$ dbifasta -idformat ncbi -directory /var/data/blast_db
> -filenames ecoli.nt -fields des -dbname ecoli_nt -release 0.0 -date
> 00/00/00
> [marcus]$ seqret ecoli_nt: -auto -stdout|head
>> AE000111 AE000111.1 Escherichia coli K-12 MG1655 section 1 of 400 of
> the complete genome
> AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
> TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
> TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
> ACAA
>
> I add a second database:
>
> [marcus]$ dbifasta -idformat ncbi -directory /var/data/blast_db
> -filenames ecoli.aa -fields des -dbname ecoli_aa -release 0.0 -date
> 00/00/00
>
> And when I seqret the old ecoli_nt I get the new ecoli_aa entries
> instead:
>
> [marcus]$ seqret ecoli_nt: -auto -stdout|head
>> AAC73112.1 (AE000111) thr operon leader peptide [Escherichia coli]
> MKRISTTITTTITITTGNGAG
>> AAC73113.1 (AE000111) aspartokinase I, homoserine dehydrogenase I
> [Escherichia coli]
> MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA
> LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA
> ALICRGEKMSIAIMAGV
>
>
> I tried to run dbifasta for both fasta files at the same time but it
> didn't work:
> dbifasta -idformat ncbi -directory /var/data/blast_db -filenames
> ecoli.nt ecoli.aa -fields des -dbname ecoli_nt ecoli_aa -release 0.0
> -date 00/00/00
>
> How can new databases be added without overwriting the old indexfiles?
>
>
> /Marcus
>
>
>
>
> On Wed, 2004-02-18 at 13:50, Gary Williams, Tel 01223 494522 wrote:
>> "Gary Williams, Tel 01223 494522" wrote:
>>>
>>> Marcus Claesson wrote:
>>>> But this doesn't work and I don't know why since I added the 'des
>>>> field'. Are queries like these suppose to work by the way?
>>>>
>>>> [marcus]$ seqret ecoli_nt:\*mitochondrio\* -auto -stdout
>>>> Error: Unable to read sequence 'ecoli_nt:*mitochondrio*'
>>>> Died: seqret terminated: Bad value for '-sequence' with -auto  
>>>> defined
>>>
>>> The correct syntax should be:
>>> seqret ecoli_nt-des:\*mitochondrio\* -auto -stdout
>>> See:
>>> http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Themes/ 
>>> UniformSequenceAddress.html#keys
>>
>> I think that the '*' are not required, so:
>> seqret ecoli_nt-des:mitochondrio -auto -stdout
>



From gwilliam at hgmp.mrc.ac.uk  Wed Feb 18 15:04:15 2004
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Wed, 18 Feb 2004 15:04:15 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
References: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk>
		 <1077032461.5582.34.camel@morpheus.ucc.ie>
		 <FB53EFC8-6160-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
		 <1077035334.5582.38.camel@morpheus.ucc.ie>
		 <11B65834-6169-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>
		 <1077111643.25361.59.camel@morpheus.ucc.ie>
		 <40336CF3.18E39E7C@hgmp.mrc.ac.uk>  <40336D9C.1E5D2AF4@hgmp.mrc.ac.uk> <1077115928.25361.94.camel@morpheus.ucc.ie>
Message-ID: <40337EEF.88E2CE65@hgmp.mrc.ac.uk>

Marcus Claesson wrote:

> How can new databases be added without overwriting the old indexfiles?

You must have the index files in separate directories because the
indices made by the dbi* programs always have the same names (acnum.hit,
acnum.trg, division.lkb, entryname.idx etc.)

If you have the database files in the same directory, you must put the
index files in other directories (maybe sub-directories?) and specify
the directory name by:
indexdirectory
See:
http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Usa/databases.html#attr
for details

-- 
Gary Williams
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494522			Fax: +44 1223 494512
E-mail: gwilliam at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk


From pmr at ebi.ac.uk  Wed Feb 18 15:07:03 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Wed, 18 Feb 2004 15:07:03 +0000
Subject: [EMBOSS] can't access databases indexed by dbifasta
In-Reply-To: <1077115928.25361.94.camel@morpheus.ucc.ie>
References: <BC57E3AA.DA41%d.m.a.martin@dundee.ac.uk>	 <1077032461.5582.34.camel@morpheus.ucc.ie>	 <FB53EFC8-6160-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>	 <1077035334.5582.38.camel@morpheus.ucc.ie>	 <11B65834-6169-11D8-8515-000A95CDA6C0@bioinfo.ulaval.ca>	 <1077111643.25361.59.camel@morpheus.ucc.ie>	 <40336CF3.18E39E7C@hgmp.mrc.ac.uk>  <40336D9C.1E5D2AF4@hgmp.mrc.ac.uk> <1077115928.25361.94.camel@morpheus.ucc.ie>
Message-ID: <40337F97.8080405@ebi.ac.uk>

Marcus Claesson wrote:

> But I continue struggling with upcoming problems and you must be tired
> of me asking questions all the time... (It's either me or the emboss man
> pages that are bad, probably a mix ;))
> 
> Anyway, when I want to create a second database ecoli_aa, dbifasta seems
> to overwrite the old indexfiles.

The index files always have the same name.

But you can put the index files in a new directory with the 
-indexdirectory option of dbifasta

The index directory goes into your database definition as

indexdirectory: "/full/path/toindex/files/"

Hope this helps

Peter Rice



From aml at computerfulfillment.com  Wed Feb 18 17:59:50 2004
From: aml at computerfulfillment.com (American Laboratory)
Date: Wed, 18 Feb 2004 12:59:50 -0500
Subject: [EMBOSS] A professional journal for you.
Message-ID: <03344902.20040218125950@computerfulfillment.com>






To Subscribe
Go To:
http://www.icainfo.com/aml/appintro.asp?acct=&amp;Renew=YES&amp;Priority=RW1003&amp;lastfour=

Following are the themes to be featured in AL: 
November Microscopy, Optics, and Image Analysis 
December Pharmaceutical Analysis, Molecular Spectroscopy, EAS 
January Annual ISC Buyers' Guide,Thermal Analysis, Gas Chromatography 
February Pittcon 2004 New Analytical Instrumentation for Separation Science and Spectroscopy 
March Advances in Laboratory Software and Data Management 
April Microchemical Analysis, Sample Preparation 




Dear Emboss, 

Please accept my invitation to continue to receive a free subscription to our journal, American Laboratory.

American Laboratory covers the disciplines of analytical and bioanalytical chemistry, drug discovery, laboratory software and informatics. Each issue features articles from leading scientists from around the world reviewing applications of instrumentation and new measurement technology.

To continue your FREE subscription to American Laboratory, please click on the following link. 

http://www.icainfo.com/aml/appintro.asp?acct=&amp;Renew=YES&amp;Priority=RW1003&amp;lastfour=


I am confident that you will enjoy our journal and find it to be of significant professional value.

I look forward to hearing from you.

Sincerely yours,

Brian Howard, Ph.D.
Editor





















International Scientific Communications, Inc.
30 Controls Drive, P.O. Box 870, Shelton, CT 06484 Tel.: 203-926-9300, 
Fax: 203-926-9310, www.iscpubs.com

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From: R-1-721447-22941564-2-8269-US2-D7857328 at xmr3.com (International Scientific Communications, Inc.)
Date: Thu, 19 Feb 2004 00:32:37 -0500
Subject: [EMBOSS] Laboratory Instrumentation News - February 2004
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From block at xmr3.com  Thu Feb 19 20:13:20 2004
From: block at xmr3.com (Customer Service)
Date: 19 Feb 2004 20:13:20 -0000
Subject: [EMBOSS] Removal Notification
Message-ID: <20040219201320.13598.qmail@xmr3.com>

By the end of the day, the address:
      emboss at embnet.org
will no longer receive email sent from:
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This change was made at the request of:
      Hegedus.Tamas at mayo.edu

If you believe that this change was made in error,
please reply to this message.


From pmr at ebi.ac.uk  Fri Feb 20 13:13:50 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 20 Feb 2004 13:13:50 +0000
Subject: [EMBOSS] Coderet
In-Reply-To: <OF7B32F5D8.E402B94A-ONCA256E28.000458A8@nre.vic.gov.au>
References: <OF7B32F5D8.E402B94A-ONCA256E28.000458A8@nre.vic.gov.au>
Message-ID: <4036080E.2040403@ebi.ac.uk>

Hi Sean

Sean.Maceachern at dpi.vic.gov.au wrote:

> I have not done any programming in c++ so I was hoping that someone
> might be able how to suggest how I can get the output from coderet to
> resemble that of NCBI's
> 
> I think it could be done by parsing the sections in BOLD from the first few lines of the feature table.
> 
> LOCUS       NM_000367               2742 bp    mRNA    linear   PRI
> 31-OCT-2000
> DEFINITION  Homo sapiens thiopurine S-methyltransferase (TPMT), mRNA.
> ACCESSION   NM_000367
> VERSION     NM_000367.1  GI:4507652
> KEYWORDS    .
> SOURCE      Homo sapiens (human)
> 
> 
> ie)
> 
> 
>>gi|4507652 Homo sapiens thiopurine S-methyltransferase (TPMT), mRNA
> 
> ATGGATGGTACAAGAACTTCACTTGACATTGAAGAGTACTCGGATACTGAGGTACAGAAA
> AACCAAGTACTAACTCTGGAAGAATGGCAAGACAAGTGGGTGAACGGCAAGACTGCTTTT
> 
> 
> Does anyone know if this already exists in a coderet option or how I would
> be able to modfiy this in the original script?

Possible .... it would be nice to have a description in the output, but 
we have to be careful where we take it from.

This is a simple REFSEQ entry with only one CDS, but coderet has to also 
work on large bacterial genome contigs.

This means we can only get the taxonomy from the top of the entry.

However, this CDS does have information in the (true) feature table:

CDS             66..803
                 /gene="TPMT"
                 /EC_number="2.1.1.67"
                 /codon_start=1
                 /product="thiopurine S-methyltransferase"
                 /protein_id="NP_000358.1"
                 /db_xref="GI:4507653"
                 /db_xref="LocusID:7172"
                 /db_xref="MIM:187680"
                 /translation="MDGTRTSL...LYLLTEK"

So, for the description line you wanted:

 >gi|4507652 Homo sapiens thiopurine S-methyltransferase (TPMT), mRNA

We can get:

"Homo" sapiens from the SOURCE line (EMBOSS already parses this)

"TPMT" from the /gene qualifier (if present)

"thiopurine S-methyltransferase" from the /product qualifier (if present)

we can also ... if other qualifiers are missing, try /note= or simply 
use the entry description and some CDS counter:
"CDS 1 from Homo sapiens thiopurine S-methyltransferase (TPMT), mRNA."

The mRNA at the end is tricky ... I would much prefer to use the feature 
type (CDS) because that is what we have.

So you would have a description (in FASTA or NCBI or any other format) of:

 >NM_000367 Homo sapiens thiopurine S-methyltransferase (TPMT), CDS

regards,

Peter Rice



From abl at computerfulfillment.com  Fri Feb 20 15:22:36 2004
From: abl at computerfulfillment.com (American Biotechnology Laboratory)
Date: Fri, 20 Feb 2004 10:22:36 -0500
Subject: [EMBOSS] A professional journal for you.
Message-ID: <65636188.20040220102236@computerfulfillment.com>






To Subscribe
Go To:
http://www.icainfo.com/aml/appintro.asp?Priority=SARAB


Following are the themes to be featured in AL: 
November Microscopy, Optics, and Image Analysis 
December Pharmaceutical Analysis, Molecular Spectroscopy, EAS 
January Annual ISC Buyers' Guide,Thermal Analysis, Gas Chromatography 
February Pittcon 2004 New Analytical Instrumentation for Separation Science and Spectroscopy 
March Advances in Laboratory Software and Data Management 
April Microchemical Analysis, Sample Preparation 




Dear Colleague, 

Please accept my invitation to receive a free subscription to our journal, American Laboratory.

American Laboratory covers the disciplines of analytical and bioanalytical chemistry, drug discovery, laboratory software and informatics. Each issue features articles from leading scientists from around the world reviewing applications of instrumentation and new measurement technology.

For your FREE subscription to American Laboratory, please click on the following link. 

http://www.icainfo.com/aml/appintro.asp?Priority=PEPAB3


I am confident that you will enjoy our journal and find it to be of significant professional value.

I look forward to hearing from you.

Sincerely yours,

Brian Howard, Ph.D.
Editor

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From pmr at ebi.ac.uk  Mon Feb 23 10:22:37 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Mon, 23 Feb 2004 10:22:37 +0000
Subject: [EMBOSS] Staden and EMBOSS 2.8.O
In-Reply-To: <2DC41140A89ED411989D00508BDCD9ED01E28CD0@bi-exsrv1.iapc.bbsrc.ac.uk>
References: <2DC41140A89ED411989D00508BDCD9ED01E28CD0@bi-exsrv1.iapc.bbsrc.ac.uk>
Message-ID: <4039D46D.6000305@ebi.ac.uk>

simon andrews (BI) wrote:

> 
>>-----Original Message-----
>>From: Guy Bottu [mailto:gbottu at ben.vub.ac.be] 
>>Subject: [EMBOSS] Staden and EMBOSS 2.8.O
>>
>>Unfortunately there is no support for Staden anymore (well, 
>>it was recently announced that James Bonfield is working 
>>at Sanger Centre, but according to the Web page he is 
>>only developing gap4, not spin). Does someone know more about it ?
> 
> 
> James recently announced that the MRC have finally agreed to release Staden under an opensource licence.  It is therefore now being hosted and developed as a sourceforge project:
> 
> http://staden.sourceforge.net/
> 
> https://sourceforge.net/projects/staden
> 
> ..therefore if you're up to making the changes yourself you can submit patches to the project, or if not you can file it as a bug which someone else will hopefully pick up.

I have updated EMBSOS in the past to produce graphics in SPIN for some 
proggrams that did not do it "normally".

I recently volunteered to update SPIN for EMBOSS 2.8.1 (due out soon) 
and will put the updates on the Staden SourceForge site and into the 
EMBOSS distribution.

James Bonfield is here on campus so we can easily coordinate this. I may 
have a volunteer to test the SPIN/EMBOSS interface - but more would be 
welcome!

regards,

Peter Rice



From mad at biol.unlp.edu.ar  Mon Feb 23 14:52:52 2004
From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=)
Date: Mon, 23 Feb 2004 11:52:52 -0300
Subject: [EMBOSS] cannot compile a single program
Message-ID: <403A13C4.4020407@biol.unlp.edu.ar>

Dear list,

I'm trying to add a program to our EMBOSS-2.6.0 installation.
These are the steps I followed:
- added clustal.c into EMBOSS_distro/emboss dir and clustal.acd under 
EMBOSS_distro/emboss/acd
- then edited EMBOSS_distro/emboss/Makefile.am and added 'clustal' to the 
'bin_PROGRAMS' section and the line 'clustal_SOURCES = clustal.c' to the same 
Makefile.am
- when doing a 'make clustal' into EMBOSS_distro/emboss dir I get this

> # make clustal
> cd .. && /bin/sh ./config.status emboss/Makefile depfiles
> config.status: creating emboss/Makefile
> config.status: executing depfiles commands
> Makefile:2179: aaindexextract.Po: No such file or directory
> Makefile:2180: abiview.Po: No such file or directory
> Makefile:2181: acdc.Po: No such file or directory
> Makefile:2182: ajtest.Po: No such file or directory
> Makefile:2183: antigenic.Po: No such file or directory
> Makefile:2184: backtranseq.Po: No such file or directory
> Makefile:2185: banana.Po: No such file or directory
> Makefile:2186: biosed.Po: No such file or directory
> Makefile:2187: btwisted.Po: No such file or directory
> Makefile:2188: cai.Po: No such file or directory
> Makefile:2189: chaos.Po: No such file or directory
> Makefile:2190: charge.Po: No such file or directory
> Makefile:2191: checktrans.Po: No such file or directory
> Makefile:2192: chips.Po: No such file or directory
> Makefile:2193: cirdna.Po: No such file or directory
> Makefile:2194: clustal.Po: No such file or directory
> Makefile:2195: codcmp.Po: No such file or directory
> Makefile:2196: coderet.Po: No such file or directory
> Makefile:2197: complex.Po: No such file or directory
> Makefile:2198: compseq.Po: No such file or directory
> Makefile:2199: cons.Po: No such file or directory
> Makefile:2200: corbatest.Po: No such file or directory
> Makefile:2201: cpgplot.Po: No such file or directory
> Makefile:2202: cpgreport.Po: No such file or directory
> Makefile:2203: cusp.Po: No such file or directory
> Makefile:2204: cutgextract.Po: No such file or directory
> Makefile:2205: cutseq.Po: No such file or directory
> Makefile:2206: dan.Po: No such file or directory
> Makefile:2207: dbiblast.Po: No such file or directory
> Makefile:2208: dbifasta.Po: No such file or directory
> Makefile:2209: dbiflat.Po: No such file or directory
> Makefile:2210: dbigcg.Po: No such file or directory
> Makefile:2211: degapseq.Po: No such file or directory
> Makefile:2212: demoalign.Po: No such file or directory
> Makefile:2213: demofeatures.Po: No such file or directory
> Makefile:2214: demolist.Po: No such file or directory
> Makefile:2215: demoreport.Po: No such file or directory
> Makefile:2216: demosequence.Po: No such file or directory
> Makefile:2217: demostring.Po: No such file or directory
> Makefile:2218: demotable.Po: No such file or directory
> Makefile:2219: descseq.Po: No such file or directory
> Makefile:2220: diffseq.Po: No such file or directory
> Makefile:2221: digest.Po: No such file or directory
> Makefile:2222: distmat.Po: No such file or directory
> Makefile:2223: dotmatcher.Po: No such file or directory
> Makefile:2224: dotpath.Po: No such file or directory
> Makefile:2225: dottup.Po: No such file or directory
> Makefile:2226: dreg.Po: No such file or directory
> Makefile:2227: einverted.Po: No such file or directory
> Makefile:2228: embossdata.Po: No such file or directory
> Makefile:2229: embossversion.Po: No such file or directory
> Makefile:2230: emma.Po: No such file or directory
> Makefile:2231: emowse.Po: No such file or directory
> Makefile:2232: entrails.Po: No such file or directory
> Makefile:2233: entret.Po: No such file or directory
> Makefile:2234: eprimer3.Po: No such file or directory
> Makefile:2235: equicktandem.Po: No such file or directory
> Makefile:2236: est2genome.Po: No such file or directory
> Makefile:2237: etandem.Po: No such file or directory
> Makefile:2238: extractfeat.Po: No such file or directory
> Makefile:2239: extractseq.Po: No such file or directory
> Makefile:2240: findkm.Po: No such file or directory
> Makefile:2241: freak.Po: No such file or directory
> Makefile:2242: fuzznuc.Po: No such file or directory
> Makefile:2243: fuzzpro.Po: No such file or directory
> Makefile:2244: fuzztran.Po: No such file or directory
> Makefile:2245: garnier.Po: No such file or directory
> Makefile:2246: geecee.Po: No such file or directory
> Makefile:2247: getorf.Po: No such file or directory
> Makefile:2248: helixturnhelix.Po: No such file or directory
> Makefile:2249: histogramtest.Po: No such file or directory
> Makefile:2250: hmoment.Po: No such file or directory
> Makefile:2251: iep.Po: No such file or directory
> Makefile:2252: infoalign.Po: No such file or directory
> Makefile:2253: infoseq.Po: No such file or directory
> Makefile:2254: intconv.Po: No such file or directory
> Makefile:2255: isochore.Po: No such file or directory
> Makefile:2256: jembossctl.Po: No such file or directory
> Makefile:2257: lindna.Po: No such file or directory
> Makefile:2258: listor.Po: No such file or directory
> Makefile:2259: marscan.Po: No such file or directory
> Makefile:2260: maskfeat.Po: No such file or directory
> Makefile:2261: maskseq.Po: No such file or directory
> Makefile:2262: matcher.Po: No such file or directory
> Makefile:2263: megamerger.Po: No such file or directory
> Makefile:2264: merger.Po: No such file or directory
> Makefile:2265: msbar.Po: No such file or directory
> Makefile:2266: mwcontam.Po: No such file or directory
> Makefile:2267: mwfilter.Po: No such file or directory
> Makefile:2268: needle.Po: No such file or directory
> Makefile:2269: newcpgreport.Po: No such file or directory
> Makefile:2270: newcpgseek.Po: No such file or directory
> Makefile:2271: newseq.Po: No such file or directory
> Makefile:2272: noreturn.Po: No such file or directory
> Makefile:2273: notseq.Po: No such file or directory
> Makefile:2274: nthseq.Po: No such file or directory
> Makefile:2275: octanol.Po: No such file or directory
> Makefile:2276: oddcomp.Po: No such file or directory
> Makefile:2277: palindrome.Po: No such file or directory
> Makefile:2278: pasteseq.Po: No such file or directory
> Makefile:2279: patmatdb.Po: No such file or directory
> Makefile:2280: patmatmotifs.Po: No such file or directory
> Makefile:2281: patmattest.Po: No such file or directory
> Makefile:2282: pepcoil.Po: No such file or directory
> Makefile:2283: pepinfo.Po: No such file or directory
> Makefile:2284: pepnet.Po: No such file or directory
> Makefile:2285: pepstats.Po: No such file or directory
> Makefile:2286: pepwheel.Po: No such file or directory
> Makefile:2287: pepwindow.Po: No such file or directory
> Makefile:2288: pepwindowall.Po: No such file or directory
> Makefile:2289: pestfind.Po: No such file or directory
> Makefile:2290: plotcon.Po: No such file or directory
> Makefile:2291: plotorf.Po: No such file or directory
> Makefile:2292: polydot.Po: No such file or directory
> Makefile:2293: preg.Po: No such file or directory
> Makefile:2294: prettyplot.Po: No such file or directory
> Makefile:2295: prettyseq.Po: No such file or directory
> Makefile:2296: prima.Po: No such file or directory
> Makefile:2297: primers.Po: No such file or directory
> Makefile:2298: primersearch.Po: No such file or directory
> Makefile:2299: printsextract.Po: No such file or directory
> Makefile:2300: profit.Po: No such file or directory
> Makefile:2301: prophecy.Po: No such file or directory
> Makefile:2302: prophet.Po: No such file or directory
> Makefile:2303: prosextract.Po: No such file or directory
> Makefile:2304: pscan.Po: No such file or directory
> Makefile:2305: rebaseextract.Po: No such file or directory
> Makefile:2306: recoder.Po: No such file or directory
> Makefile:2307: redata.Po: No such file or directory
> Makefile:2308: remap.Po: No such file or directory
> Makefile:2309: restover.Po: No such file or directory
> Makefile:2310: restrict.Po: No such file or directory
> Makefile:2311: revseq.Po: No such file or directory
> Makefile:2312: seealso.Po: No such file or directory
> Makefile:2313: seqinfo.Po: No such file or directory
> Makefile:2314: seqmatchall.Po: No such file or directory
> Makefile:2315: seqret.Po: No such file or directory
> Makefile:2316: seqretall.Po: No such file or directory
> Makefile:2317: seqretallfeat.Po: No such file or directory
> Makefile:2318: seqretset.Po: No such file or directory
> Makefile:2319: seqretsingle.Po: No such file or directory
> Makefile:2320: seqretsplit.Po: No such file or directory
> Makefile:2321: showalign.Po: No such file or directory
> Makefile:2322: showdb.Po: No such file or directory
> Makefile:2323: showfeat.Po: No such file or directory
> Makefile:2324: showorf.Po: No such file or directory
> Makefile:2325: showseq.Po: No such file or directory
> Makefile:2326: shuffleseq.Po: No such file or directory
> Makefile:2327: sigcleave.Po: No such file or directory
> Makefile:2328: silent.Po: No such file or directory
> Makefile:2329: sirna.Po: No such file or directory
> Makefile:2330: sixpack.Po: No such file or directory
> Makefile:2331: skipseq.Po: No such file or directory
> Makefile:2332: splitter.Po: No such file or directory
> Makefile:2333: stretcher.Po: No such file or directory
> Makefile:2334: stssearch.Po: No such file or directory
> Makefile:2335: supermatcher.Po: No such file or directory
> Makefile:2336: syco.Po: No such file or directory
> Makefile:2337: testplot.Po: No such file or directory
> Makefile:2338: textsearch.Po: No such file or directory
> Makefile:2339: tfextract.Po: No such file or directory
> Makefile:2340: tfm.Po: No such file or directory
> Makefile:2341: tfscan.Po: No such file or directory
> Makefile:2342: tmap.Po: No such file or directory
> Makefile:2343: tranalign.Po: No such file or directory
> Makefile:2344: transeq.Po: No such file or directory
> Makefile:2345: treetypedisplay.Po: No such file or directory
> Makefile:2346: trimest.Po: No such file or directory
> Makefile:2347: trimseq.Po: No such file or directory
> Makefile:2348: twofeat.Po: No such file or directory
> Makefile:2349: union.Po: No such file or directory
> Makefile:2350: vectorstrip.Po: No such file or directory
> Makefile:2351: water.Po: No such file or directory
> Makefile:2352: whichdb.Po: No such file or directory
> Makefile:2353: wobble.Po: No such file or directory
> Makefile:2354: wordcount.Po: No such file or directory
> Makefile:2355: wordmatch.Po: No such file or directory
> Makefile:2356: wossname.Po: No such file or directory
> Makefile:2357: yank.Po: No such file or directory
> make: *** No rule to make target `yank.Po'.  Stop.
> #

What am I missing?

Regards,

martin

-- 
Mart?n Sarachu
mad at biol.unlp.edu.ar
EMBNet Argentina
http://www.ar.embnet.org


From d.gatherer at vir.gla.ac.uk  Mon Feb 23 15:06:11 2004
From: d.gatherer at vir.gla.ac.uk (Derek Gatherer)
Date: Mon, 23 Feb 2004 15:06:11 +0000
Subject: [EMBOSS] cannot compile a single program
In-Reply-To: <403A13C4.4020407@biol.unlp.edu.ar>
Message-ID: <5.2.1.1.1.20040223145844.00acecd0@udcf.gla.ac.uk>

Hi

You need to be working from the cvs version of emboss:

 >cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss login
 >cvs
 >cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss checkout emboss
 >cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss logout

Assuming you have got this, you need to do what you did, ie. add the code 
in the correct place and modify the makefile appropriately, and then go to 
the correct directory and enter:

 >aclocal -I m4
 >autoconf -v
 >automake -a
 >./configure
 >make
 >make check
 >make install
 >make clean

You'll need up to date versions of autoconf and automake.  We add lots of 
local code - it's convoluted to do all this, but it always works.

Cheers
Derek

At 11:52 23/02/2004 -0300, you wrote:
>Dear list,
>
>I'm trying to add a program to our EMBOSS-2.6.0 installation.
>These are the steps I followed:
>- added clustal.c into EMBOSS_distro/emboss dir and clustal.acd under 
>EMBOSS_distro/emboss/acd
>- then edited EMBOSS_distro/emboss/Makefile.am and added 'clustal' to the 
>'bin_PROGRAMS' section and the line 'clustal_SOURCES = clustal.c' to the 
>same Makefile.am
>- when doing a 'make clustal' into EMBOSS_distro/emboss dir I get this
>
>># make clustal
>>cd .. && /bin/sh ./config.status emboss/Makefile depfiles
>>config.status: creating emboss/Makefile
>>config.status: executing depfiles commands
>>Makefile:2179: aaindexextract.Po: No such file or directory
>>Makefile:2180: abiview.Po: No such file or directory
>>Makefile:2181: acdc.Po: No such file or directory
>>Makefile:2182: ajtest.Po: No such file or directory
>>Makefile:2183: antigenic.Po: No such file or directory
>>Makefile:2184: backtranseq.Po: No such file or directory
>>Makefile:2185: banana.Po: No such file or directory
>>Makefile:2186: biosed.Po: No such file or directory
>>Makefile:2187: btwisted.Po: No such file or directory
>>Makefile:2188: cai.Po: No such file or directory
>>Makefile:2189: chaos.Po: No such file or directory
>>Makefile:2190: charge.Po: No such file or directory
>>Makefile:2191: checktrans.Po: No such file or directory
>>Makefile:2192: chips.Po: No such file or directory
>>Makefile:2193: cirdna.Po: No such file or directory
>>Makefile:2194: clustal.Po: No such file or directory
>>Makefile:2195: codcmp.Po: No such file or directory
>>Makefile:2196: coderet.Po: No such file or directory
>>Makefile:2197: complex.Po: No such file or directory
>>Makefile:2198: compseq.Po: No such file or directory
>>Makefile:2199: cons.Po: No such file or directory
>>Makefile:2200: corbatest.Po: No such file or directory
>>Makefile:2201: cpgplot.Po: No such file or directory
>>Makefile:2202: cpgreport.Po: No such file or directory
>>Makefile:2203: cusp.Po: No such file or directory
>>Makefile:2204: cutgextract.Po: No such file or directory
>>Makefile:2205: cutseq.Po: No such file or directory
>>Makefile:2206: dan.Po: No such file or directory
>>Makefile:2207: dbiblast.Po: No such file or directory
>>Makefile:2208: dbifasta.Po: No such file or directory
>>Makefile:2209: dbiflat.Po: No such file or directory
>>Makefile:2210: dbigcg.Po: No such file or directory
>>Makefile:2211: degapseq.Po: No such file or directory
>>Makefile:2212: demoalign.Po: No such file or directory
>>Makefile:2213: demofeatures.Po: No such file or directory
>>Makefile:2214: demolist.Po: No such file or directory
>>Makefile:2215: demoreport.Po: No such file or directory
>>Makefile:2216: demosequence.Po: No such file or directory
>>Makefile:2217: demostring.Po: No such file or directory
>>Makefile:2218: demotable.Po: No such file or directory
>>Makefile:2219: descseq.Po: No such file or directory
>>Makefile:2220: diffseq.Po: No such file or directory
>>Makefile:2221: digest.Po: No such file or directory
>>Makefile:2222: distmat.Po: No such file or directory
>>Makefile:2223: dotmatcher.Po: No such file or directory
>>Makefile:2224: dotpath.Po: No such file or directory
>>Makefile:2225: dottup.Po: No such file or directory
>>Makefile:2226: dreg.Po: No such file or directory
>>Makefile:2227: einverted.Po: No such file or directory
>>Makefile:2228: embossdata.Po: No such file or directory
>>Makefile:2229: embossversion.Po: No such file or directory
>>Makefile:2230: emma.Po: No such file or directory
>>Makefile:2231: emowse.Po: No such file or directory
>>Makefile:2232: entrails.Po: No such file or directory
>>Makefile:2233: entret.Po: No such file or directory
>>Makefile:2234: eprimer3.Po: No such file or directory
>>Makefile:2235: equicktandem.Po: No such file or directory
>>Makefile:2236: est2genome.Po: No such file or directory
>>Makefile:2237: etandem.Po: No such file or directory
>>Makefile:2238: extractfeat.Po: No such file or directory
>>Makefile:2239: extractseq.Po: No such file or directory
>>Makefile:2240: findkm.Po: No such file or directory
>>Makefile:2241: freak.Po: No such file or directory
>>Makefile:2242: fuzznuc.Po: No such file or directory
>>Makefile:2243: fuzzpro.Po: No such file or directory
>>Makefile:2244: fuzztran.Po: No such file or directory
>>Makefile:2245: garnier.Po: No such file or directory
>>Makefile:2246: geecee.Po: No such file or directory
>>Makefile:2247: getorf.Po: No such file or directory
>>Makefile:2248: helixturnhelix.Po: No such file or directory
>>Makefile:2249: histogramtest.Po: No such file or directory
>>Makefile:2250: hmoment.Po: No such file or directory
>>Makefile:2251: iep.Po: No such file or directory
>>Makefile:2252: infoalign.Po: No such file or directory
>>Makefile:2253: infoseq.Po: No such file or directory
>>Makefile:2254: intconv.Po: No such file or directory
>>Makefile:2255: isochore.Po: No such file or directory
>>Makefile:2256: jembossctl.Po: No such file or directory
>>Makefile:2257: lindna.Po: No such file or directory
>>Makefile:2258: listor.Po: No such file or directory
>>Makefile:2259: marscan.Po: No such file or directory
>>Makefile:2260: maskfeat.Po: No such file or directory
>>Makefile:2261: maskseq.Po: No such file or directory
>>Makefile:2262: matcher.Po: No such file or directory
>>Makefile:2263: megamerger.Po: No such file or directory
>>Makefile:2264: merger.Po: No such file or directory
>>Makefile:2265: msbar.Po: No such file or directory
>>Makefile:2266: mwcontam.Po: No such file or directory
>>Makefile:2267: mwfilter.Po: No such file or directory
>>Makefile:2268: needle.Po: No such file or directory
>>Makefile:2269: newcpgreport.Po: No such file or directory
>>Makefile:2270: newcpgseek.Po: No such file or directory
>>Makefile:2271: newseq.Po: No such file or directory
>>Makefile:2272: noreturn.Po: No such file or directory
>>Makefile:2273: notseq.Po: No such file or directory
>>Makefile:2274: nthseq.Po: No such file or directory
>>Makefile:2275: octanol.Po: No such file or directory
>>Makefile:2276: oddcomp.Po: No such file or directory
>>Makefile:2277: palindrome.Po: No such file or directory
>>Makefile:2278: pasteseq.Po: No such file or directory
>>Makefile:2279: patmatdb.Po: No such file or directory
>>Makefile:2280: patmatmotifs.Po: No such file or directory
>>Makefile:2281: patmattest.Po: No such file or directory
>>Makefile:2282: pepcoil.Po: No such file or directory
>>Makefile:2283: pepinfo.Po: No such file or directory
>>Makefile:2284: pepnet.Po: No such file or directory
>>Makefile:2285: pepstats.Po: No such file or directory
>>Makefile:2286: pepwheel.Po: No such file or directory
>>Makefile:2287: pepwindow.Po: No such file or directory
>>Makefile:2288: pepwindowall.Po: No such file or directory
>>Makefile:2289: pestfind.Po: No such file or directory
>>Makefile:2290: plotcon.Po: No such file or directory
>>Makefile:2291: plotorf.Po: No such file or directory
>>Makefile:2292: polydot.Po: No such file or directory
>>Makefile:2293: preg.Po: No such file or directory
>>Makefile:2294: prettyplot.Po: No such file or directory
>>Makefile:2295: prettyseq.Po: No such file or directory
>>Makefile:2296: prima.Po: No such file or directory
>>Makefile:2297: primers.Po: No such file or directory
>>Makefile:2298: primersearch.Po: No such file or directory
>>Makefile:2299: printsextract.Po: No such file or directory
>>Makefile:2300: profit.Po: No such file or directory
>>Makefile:2301: prophecy.Po: No such file or directory
>>Makefile:2302: prophet.Po: No such file or directory
>>Makefile:2303: prosextract.Po: No such file or directory
>>Makefile:2304: pscan.Po: No such file or directory
>>Makefile:2305: rebaseextract.Po: No such file or directory
>>Makefile:2306: recoder.Po: No such file or directory
>>Makefile:2307: redata.Po: No such file or directory
>>Makefile:2308: remap.Po: No such file or directory
>>Makefile:2309: restover.Po: No such file or directory
>>Makefile:2310: restrict.Po: No such file or directory
>>Makefile:2311: revseq.Po: No such file or directory
>>Makefile:2312: seealso.Po: No such file or directory
>>Makefile:2313: seqinfo.Po: No such file or directory
>>Makefile:2314: seqmatchall.Po: No such file or directory
>>Makefile:2315: seqret.Po: No such file or directory
>>Makefile:2316: seqretall.Po: No such file or directory
>>Makefile:2317: seqretallfeat.Po: No such file or directory
>>Makefile:2318: seqretset.Po: No such file or directory
>>Makefile:2319: seqretsingle.Po: No such file or directory
>>Makefile:2320: seqretsplit.Po: No such file or directory
>>Makefile:2321: showalign.Po: No such file or directory
>>Makefile:2322: showdb.Po: No such file or directory
>>Makefile:2323: showfeat.Po: No such file or directory
>>Makefile:2324: showorf.Po: No such file or directory
>>Makefile:2325: showseq.Po: No such file or directory
>>Makefile:2326: shuffleseq.Po: No such file or directory
>>Makefile:2327: sigcleave.Po: No such file or directory
>>Makefile:2328: silent.Po: No such file or directory
>>Makefile:2329: sirna.Po: No such file or directory
>>Makefile:2330: sixpack.Po: No such file or directory
>>Makefile:2331: skipseq.Po: No such file or directory
>>Makefile:2332: splitter.Po: No such file or directory
>>Makefile:2333: stretcher.Po: No such file or directory
>>Makefile:2334: stssearch.Po: No such file or directory
>>Makefile:2335: supermatcher.Po: No such file or directory
>>Makefile:2336: syco.Po: No such file or directory
>>Makefile:2337: testplot.Po: No such file or directory
>>Makefile:2338: textsearch.Po: No such file or directory
>>Makefile:2339: tfextract.Po: No such file or directory
>>Makefile:2340: tfm.Po: No such file or directory
>>Makefile:2341: tfscan.Po: No such file or directory
>>Makefile:2342: tmap.Po: No such file or directory
>>Makefile:2343: tranalign.Po: No such file or directory
>>Makefile:2344: transeq.Po: No such file or directory
>>Makefile:2345: treetypedisplay.Po: No such file or directory
>>Makefile:2346: trimest.Po: No such file or directory
>>Makefile:2347: trimseq.Po: No such file or directory
>>Makefile:2348: twofeat.Po: No such file or directory
>>Makefile:2349: union.Po: No such file or directory
>>Makefile:2350: vectorstrip.Po: No such file or directory
>>Makefile:2351: water.Po: No such file or directory
>>Makefile:2352: whichdb.Po: No such file or directory
>>Makefile:2353: wobble.Po: No such file or directory
>>Makefile:2354: wordcount.Po: No such file or directory
>>Makefile:2355: wordmatch.Po: No such file or directory
>>Makefile:2356: wossname.Po: No such file or directory
>>Makefile:2357: yank.Po: No such file or directory
>>make: *** No rule to make target `yank.Po'.  Stop.
>>#
>
>What am I missing?
>
>Regards,
>
>martin
>
>--
>Mart?n Sarachu
>mad at biol.unlp.edu.ar
>EMBNet Argentina
>http://www.ar.embnet.org



From mad at biol.unlp.edu.ar  Tue Feb 24 13:27:06 2004
From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=)
Date: Tue, 24 Feb 2004 10:27:06 -0300
Subject: [EMBOSS] Cannot configure, auto* tools problem?
Message-ID: <403B512A.10003@biol.unlp.edu.ar>

Dear list,

when running 'configure' I'm getting some errors...

> # ./configure --prefix=/usr/local/emboss
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
> checking build system type... i686-pc-linux-gnu
> checking host system type... i686-pc-linux-gnu
> checking for style of include used by make... GNU
> checking for gcc... gcc
> checking for C compiler default output... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking dependency style of gcc... gcc3
> checking for ld used by GCC... /usr/bin/ld
> checking if the linker (/usr/bin/ld) is GNU ld... yes
> checking for /usr/bin/ld option to reload object files... -r
> checking for BSD-compatible nm... /usr/bin/nm -B
> checking whether ln -s works... yes
> checking how to recognise dependant libraries... pass_all
> checking command to parse /usr/bin/nm -B output... ok
> checking how to run the C preprocessor... gcc -E
> checking for egrep... grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking dlfcn.h usability... yes
> checking dlfcn.h presence... yes
> checking for dlfcn.h... yes
> checking for ranlib... ranlib
> checking for strip... strip
> checking for objdir... .libs
> checking for gcc option to produce PIC... -fPIC
> checking if gcc PIC flag -fPIC works... yes
> checking if gcc static flag -static works... yes
> checking if gcc supports -c -o file.o... yes
> checking if gcc supports -c -o file.lo... yes
> checking if gcc supports -fno-rtti -fno-exceptions... yes
> checking whether the linker (/usr/bin/ld) supports shared libraries... yes
> checking how to hardcode library paths into programs... immediate
> checking whether stripping libraries is possible... yes
> checking dynamic linker characteristics... GNU/Linux ld.so
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... yes
> checking whether to build static libraries... yes
> checking whether -lc should be explicitly linked in... no
> creating libtool
> checking for gawk... (cached) gawk
> checking for gcc... (cached) gcc
> checking whether we are using the GNU C compiler... (cached) yes
> checking whether gcc accepts -g... (cached) yes
> checking for gcc option to accept ANSI C... (cached) none needed
> checking dependency style of gcc... (cached) gcc3
> checking how to run the C preprocessor... gcc -E
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether ln -s works... yes
> checking whether make sets $(MAKE)... (cached) yes
> checking for ranlib... (cached) ranlib
> checking for X... libraries /usr/X11R6/lib, headers /usr/X11R6/include
> checking for gethostbyname... yes
> checking for connect... yes
> checking for remove... yes
> checking for shmat... yes
> checking for IceConnectionNumber in -lICE... yes
> checking for dirent.h that defines DIR... yes
> checking for library containing opendir... none required
> checking for ANSI C header files... (cached) yes
> checking for unistd.h... (cached) yes
> checking for an ANSI C-conforming const... yes
> checking for pid_t... yes
> checking for size_t... yes
> checking whether struct tm is in sys/time.h or time.h... time.h
> checking whether getpgrp requires zero arguments... yes
> checking for strftime... yes
> checking for unistd.h... (cached) yes
> checking vfork.h usability... no
> checking vfork.h presence... no
> checking for vfork.h... no
> checking for fork... yes
> checking for vfork... yes
> checking for working fork... yes
> checking for working vfork... (cached) yes
> checking for vprintf... yes
> checking for _doprnt... no
> checking for memmove... yes
> ./configure: LF_EMBOSS_PATH_XLIB: command not found  << HERE
> checking for gethostbyname in -lc... yes
> checking for socket in -lc... yes
> checking for main in -lm... yes
> ./configure: CHECK_PNGDRIVER: command not found  << HERE
> ./configure: CHECK_JAVA: command not found  << HERE
> ./configure: CHECK_JAVAOS: command not found  << HERE
> ./configure: CHECK_AUTH: command not found  << HERE
> checking for purify... no
> ./configure: CHECK_THREADS: command not found  << HERE
> configure: creating ./config.status
> config.status: creating plplot/Makefile
> config.status: creating plplot/lib/Makefile
> config.status: creating nucleus/Makefile
> config.status: creating ajax/Makefile
> config.status: creating emboss/Makefile
> config.status: creating emboss/acd/Makefile
> config.status: creating test/Makefile
> config.status: creating test/data/Makefile
> config.status: creating test/embl/Makefile
> config.status: creating test/genbank/Makefile
> config.status: creating test/gb/Makefile
> config.status: creating test/pir/Makefile
> config.status: creating test/swiss/Makefile
> config.status: creating test/swnew/Makefile
> config.status: creating test/wormpep/Makefile
> config.status: creating emboss/data/Makefile
> config.status: creating emboss/data/AAINDEX/Makefile
> config.status: creating emboss/data/CODONS/Makefile
> config.status: creating emboss/data/REBASE/Makefile
> config.status: creating emboss/data/PRINTS/Makefile
> config.status: creating emboss/data/PROSITE/Makefile
> config.status: creating doc/Makefile
> config.status: creating doc/manuals/Makefile
> config.status: creating doc/tutorials/Makefile
> config.status: creating doc/programs/Makefile
> config.status: creating doc/programs/html/Makefile
> config.status: creating doc/programs/text/Makefile
> config.status: creating jemboss/Makefile
> config.status: creating jemboss/api/Makefile
> config.status: creating jemboss/api/org/Makefile
> config.status: creating jemboss/api/org/emboss/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/gui/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/gui/filetree/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/gui/form/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/gui/sequenceChooser/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/gui/startup/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/parser/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/parser/acd/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/programs/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/soap/Makefile
> config.status: creating jemboss/images/Makefile
> config.status: creating jemboss/lib/Makefile
> config.status: creating jemboss/lib/axis/Makefile
> config.status: creating jemboss/org/Makefile
> config.status: creating jemboss/org/emboss/Makefile
> config.status: creating jemboss/org/emboss/jemboss/Makefile
> config.status: creating jemboss/org/emboss/jemboss/gui/Makefile
> config.status: creating jemboss/org/emboss/jemboss/gui/filetree/Makefile
> config.status: creating jemboss/org/emboss/jemboss/gui/form/Makefile
> config.status: creating jemboss/org/emboss/jemboss/gui/startup/Makefile
> config.status: creating jemboss/org/emboss/jemboss/gui/sequenceChooser/Makefile
> config.status: creating jemboss/org/emboss/jemboss/parser/Makefile
> config.status: creating jemboss/org/emboss/jemboss/parser/acd/Makefile
> config.status: creating jemboss/org/emboss/jemboss/programs/Makefile
> config.status: creating jemboss/org/emboss/jemboss/server/Makefile
> config.status: creating jemboss/org/emboss/jemboss/soap/Makefile
> config.status: creating jemboss/resources/Makefile
> config.status: creating jemboss/utils/Makefile
> config.status: creating Makefile
> config.status: executing depfiles commands
> #

then when doing 'make'...

> # make
> Making all in plplot
> make[1]: Entering directory `/home/work/EMBOSS/test/plplot'
> Making all in lib
> make[2]: Entering directory `/home/work/EMBOSS/test/plplot/lib'
> make[2]: Nothing to be done for `all'.
> make[2]: Leaving directory `/home/work/EMBOSS/test/plplot/lib'
> make[2]: Entering directory `/home/work/EMBOSS/test/plplot'
> source='pdfutils.c' object='pdfutils.lo' libtool=yes \
> depfile='.deps/pdfutils.Plo' tmpdepfile='.deps/pdfutils.TPlo' \
> depmode=gcc3 /bin/sh ../depcomp \
> /bin/sh ../libtool --mode=compile gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2.6.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1  -I. -I. -I/usr/X11R6/include -I./ -I/usr/include/gd    -g -O2 -c -o pdfutils.lo `test -f pdfutils.c || echo './'`pdfutils.c
> ../libtool: s%^.*/%%: No such file or directory
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> : compile: cannot determine name of library object from `'
> make[2]: *** [pdfutils.lo] Error 1
> make[2]: Leaving directory `/home/work/EMBOSS/test/plplot'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/home/work/EMBOSS/test/plplot'
> make: *** [all-recursive] Error 1
> #

The system is a Redhat 7.3, autoconf 2.13 RPM, automake 1.4p5 RPM
Any hints of what is the problem?
Thanks.

Regards,

martin

-- 
Mart?n Sarachu
mad at biol.unlp.edu.ar
EMBNet Argentina
http://www.ar.embnet.org


From mad at biol.unlp.edu.ar  Tue Feb 24 14:24:10 2004
From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=)
Date: Tue, 24 Feb 2004 11:24:10 -0300
Subject: [EMBOSS] cannot compile a single program
In-Reply-To: <5.2.1.1.1.20040224135709.0315dd68@udcf.gla.ac.uk>
References: <5.2.1.1.1.20040223145844.00acecd0@udcf.gla.ac.uk> <5.2.1.1.1.20040223145844.00acecd0@udcf.gla.ac.uk> <5.2.1.1.1.20040224135709.0315dd68@udcf.gla.ac.uk>
Message-ID: <403B5E8A.8000002@biol.unlp.edu.ar>

Hi

installed libtool-1.5.2 and yet the same errors

Regards,

martin

Derek Gatherer wrote:
> Hi
> 
> You will need libtool as well, by the looks of it.
> http://www.gnu.org/software/libtool/
> 
> Hope this helps
> Derek
> 
> 
> At 09:28 24/02/2004 -0300, you wrote:
> 
>> Hi Derek,
>>
>> thanks for your help. I've got other problems though, I followed your 
>> steps and when doing make I get
>>
>>> # make
>>> Making all in plplot
>>> make[1]: Entering directory `/home/work/EMBOSS/test/plplot'
>>> Making all in lib
>>> make[2]: Entering directory `/home/work/EMBOSS/test/plplot/lib'
>>> make[2]: Nothing to be done for `all'.
>>> make[2]: Leaving directory `/home/work/EMBOSS/test/plplot/lib'
>>> make[2]: Entering directory `/home/work/EMBOSS/test/plplot'
>>> source='pdfutils.c' object='pdfutils.lo' libtool=yes \
>>> depfile='.deps/pdfutils.Plo' tmpdepfile='.deps/pdfutils.TPlo' \
>>> depmode=gcc3 /bin/sh ../depcomp \
>>> /bin/sh ../libtool --mode=compile gcc -DPACKAGE_NAME=\"\" 
>>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
>>> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2.6.0\" 
>>> -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 
>>> -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 
>>> -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 
>>> -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 
>>> -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 
>>> -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 
>>> -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 
>>> -DHAVE_LIBM=1  -I. -I. -I/usr/X11R6/include -I./ -I/usr/include/gd    
>>> -g -O2 -c -o pdfutils.lo `test -f pdfutils.c || echo './'`pdfutils.c
>>> ../libtool: s%^.*/%%: No such file or directory
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> : compile: cannot determine name of library object from `'
>>> make[2]: *** [pdfutils.lo] Error 1
>>> make[2]: Leaving directory `/home/work/EMBOSS/test/plplot'
>>> make[1]: *** [all-recursive] Error 1
>>> make[1]: Leaving directory `/home/work/EMBOSS/test/plplot'
>>> make: *** [all-recursive] Error 1
>>> #
>>
>>
>> Can you help me with this? Thank you.
>>
>>
>> Regards,
>>
>> martin
>>
>>
>> Derek Gatherer wrote:
>>
>>> Hi
>>> You need to be working from the cvs version of emboss:
>>>  >cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss login
>>>  >cvs
>>>  >cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss 
>>> checkout emboss
>>>  >cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss logout
>>> Assuming you have got this, you need to do what you did, ie. add the 
>>> code in the correct place and modify the makefile appropriately, and 
>>> then go to the correct directory and enter:
>>>  >aclocal -I m4
>>>  >autoconf -v
>>>  >automake -a
>>>  >./configure
>>>  >make
>>>  >make check
>>>  >make install
>>>  >make clean
>>> You'll need up to date versions of autoconf and automake.  We add 
>>> lots of local code - it's convoluted to do all this, but it always 
>>> works.
>>> Cheers
>>> Derek
>>> At 11:52 23/02/2004 -0300, you wrote:
>>>
>>>> Dear list,
>>>>
>>>> I'm trying to add a program to our EMBOSS-2.6.0 installation.
>>>> These are the steps I followed:
>>>> - added clustal.c into EMBOSS_distro/emboss dir and clustal.acd 
>>>> under EMBOSS_distro/emboss/acd
>>>> - then edited EMBOSS_distro/emboss/Makefile.am and added 'clustal' 
>>>> to the 'bin_PROGRAMS' section and the line 'clustal_SOURCES = 
>>>> clustal.c' to the same Makefile.am
>>>> - when doing a 'make clustal' into EMBOSS_distro/emboss dir I get this
>>>>
>>>>> # make clustal
>>>>> cd .. && /bin/sh ./config.status emboss/Makefile depfiles
>>>>> config.status: creating emboss/Makefile
>>>>> config.status: executing depfiles commands
>>>>> Makefile:2179: aaindexextract.Po: No such file or directory
>>>>> Makefile:2180: abiview.Po: No such file or directory
>>>>> Makefile:2181: acdc.Po: No such file or directory
>>>>> Makefile:2182: ajtest.Po: No such file or directory
>>>>> Makefile:2183: antigenic.Po: No such file or directory
>>>>> Makefile:2184: backtranseq.Po: No such file or directory
>>>>> Makefile:2185: banana.Po: No such file or directory
>>>>> Makefile:2186: biosed.Po: No such file or directory
>>>>> Makefile:2187: btwisted.Po: No such file or directory
>>>>> Makefile:2188: cai.Po: No such file or directory
>>>>> Makefile:2189: chaos.Po: No such file or directory
>>>>> Makefile:2190: charge.Po: No such file or directory
>>>>> Makefile:2191: checktrans.Po: No such file or directory
>>>>> Makefile:2192: chips.Po: No such file or directory
>>>>> Makefile:2193: cirdna.Po: No such file or directory
>>>>> Makefile:2194: clustal.Po: No such file or directory
>>>>> Makefile:2195: codcmp.Po: No such file or directory
>>>>> Makefile:2196: coderet.Po: No such file or directory
>>>>> Makefile:2197: complex.Po: No such file or directory
>>>>> Makefile:2198: compseq.Po: No such file or directory
>>>>> Makefile:2199: cons.Po: No such file or directory
>>>>> Makefile:2200: corbatest.Po: No such file or directory
>>>>> Makefile:2201: cpgplot.Po: No such file or directory
>>>>> Makefile:2202: cpgreport.Po: No such file or directory
>>>>> Makefile:2203: cusp.Po: No such file or directory
>>>>> Makefile:2204: cutgextract.Po: No such file or directory
>>>>> Makefile:2205: cutseq.Po: No such file or directory
>>>>> Makefile:2206: dan.Po: No such file or directory
>>>>> Makefile:2207: dbiblast.Po: No such file or directory
>>>>> Makefile:2208: dbifasta.Po: No such file or directory
>>>>> Makefile:2209: dbiflat.Po: No such file or directory
>>>>> Makefile:2210: dbigcg.Po: No such file or directory
>>>>> Makefile:2211: degapseq.Po: No such file or directory
>>>>> Makefile:2212: demoalign.Po: No such file or directory
>>>>> Makefile:2213: demofeatures.Po: No such file or directory
>>>>> Makefile:2214: demolist.Po: No such file or directory
>>>>> Makefile:2215: demoreport.Po: No such file or directory
>>>>> Makefile:2216: demosequence.Po: No such file or directory
>>>>> Makefile:2217: demostring.Po: No such file or directory
>>>>> Makefile:2218: demotable.Po: No such file or directory
>>>>> Makefile:2219: descseq.Po: No such file or directory
>>>>> Makefile:2220: diffseq.Po: No such file or directory
>>>>> Makefile:2221: digest.Po: No such file or directory
>>>>> Makefile:2222: distmat.Po: No such file or directory
>>>>> Makefile:2223: dotmatcher.Po: No such file or directory
>>>>> Makefile:2224: dotpath.Po: No such file or directory
>>>>> Makefile:2225: dottup.Po: No such file or directory
>>>>> Makefile:2226: dreg.Po: No such file or directory
>>>>> Makefile:2227: einverted.Po: No such file or directory
>>>>> Makefile:2228: embossdata.Po: No such file or directory
>>>>> Makefile:2229: embossversion.Po: No such file or directory
>>>>> Makefile:2230: emma.Po: No such file or directory
>>>>> Makefile:2231: emowse.Po: No such file or directory
>>>>> Makefile:2232: entrails.Po: No such file or directory
>>>>> Makefile:2233: entret.Po: No such file or directory
>>>>> Makefile:2234: eprimer3.Po: No such file or directory
>>>>> Makefile:2235: equicktandem.Po: No such file or directory
>>>>> Makefile:2236: est2genome.Po: No such file or directory
>>>>> Makefile:2237: etandem.Po: No such file or directory
>>>>> Makefile:2238: extractfeat.Po: No such file or directory
>>>>> Makefile:2239: extractseq.Po: No such file or directory
>>>>> Makefile:2240: findkm.Po: No such file or directory
>>>>> Makefile:2241: freak.Po: No such file or directory
>>>>> Makefile:2242: fuzznuc.Po: No such file or directory
>>>>> Makefile:2243: fuzzpro.Po: No such file or directory
>>>>> Makefile:2244: fuzztran.Po: No such file or directory
>>>>> Makefile:2245: garnier.Po: No such file or directory
>>>>> Makefile:2246: geecee.Po: No such file or directory
>>>>> Makefile:2247: getorf.Po: No such file or directory
>>>>> Makefile:2248: helixturnhelix.Po: No such file or directory
>>>>> Makefile:2249: histogramtest.Po: No such file or directory
>>>>> Makefile:2250: hmoment.Po: No such file or directory
>>>>> Makefile:2251: iep.Po: No such file or directory
>>>>> Makefile:2252: infoalign.Po: No such file or directory
>>>>> Makefile:2253: infoseq.Po: No such file or directory
>>>>> Makefile:2254: intconv.Po: No such file or directory
>>>>> Makefile:2255: isochore.Po: No such file or directory
>>>>> Makefile:2256: jembossctl.Po: No such file or directory
>>>>> Makefile:2257: lindna.Po: No such file or directory
>>>>> Makefile:2258: listor.Po: No such file or directory
>>>>> Makefile:2259: marscan.Po: No such file or directory
>>>>> Makefile:2260: maskfeat.Po: No such file or directory
>>>>> Makefile:2261: maskseq.Po: No such file or directory
>>>>> Makefile:2262: matcher.Po: No such file or directory
>>>>> Makefile:2263: megamerger.Po: No such file or directory
>>>>> Makefile:2264: merger.Po: No such file or directory
>>>>> Makefile:2265: msbar.Po: No such file or directory
>>>>> Makefile:2266: mwcontam.Po: No such file or directory
>>>>> Makefile:2267: mwfilter.Po: No such file or directory
>>>>> Makefile:2268: needle.Po: No such file or directory
>>>>> Makefile:2269: newcpgreport.Po: No such file or directory
>>>>> Makefile:2270: newcpgseek.Po: No such file or directory
>>>>> Makefile:2271: newseq.Po: No such file or directory
>>>>> Makefile:2272: noreturn.Po: No such file or directory
>>>>> Makefile:2273: notseq.Po: No such file or directory
>>>>> Makefile:2274: nthseq.Po: No such file or directory
>>>>> Makefile:2275: octanol.Po: No such file or directory
>>>>> Makefile:2276: oddcomp.Po: No such file or directory
>>>>> Makefile:2277: palindrome.Po: No such file or directory
>>>>> Makefile:2278: pasteseq.Po: No such file or directory
>>>>> Makefile:2279: patmatdb.Po: No such file or directory
>>>>> Makefile:2280: patmatmotifs.Po: No such file or directory
>>>>> Makefile:2281: patmattest.Po: No such file or directory
>>>>> Makefile:2282: pepcoil.Po: No such file or directory
>>>>> Makefile:2283: pepinfo.Po: No such file or directory
>>>>> Makefile:2284: pepnet.Po: No such file or directory
>>>>> Makefile:2285: pepstats.Po: No such file or directory
>>>>> Makefile:2286: pepwheel.Po: No such file or directory
>>>>> Makefile:2287: pepwindow.Po: No such file or directory
>>>>> Makefile:2288: pepwindowall.Po: No such file or directory
>>>>> Makefile:2289: pestfind.Po: No such file or directory
>>>>> Makefile:2290: plotcon.Po: No such file or directory
>>>>> Makefile:2291: plotorf.Po: No such file or directory
>>>>> Makefile:2292: polydot.Po: No such file or directory
>>>>> Makefile:2293: preg.Po: No such file or directory
>>>>> Makefile:2294: prettyplot.Po: No such file or directory
>>>>> Makefile:2295: prettyseq.Po: No such file or directory
>>>>> Makefile:2296: prima.Po: No such file or directory
>>>>> Makefile:2297: primers.Po: No such file or directory
>>>>> Makefile:2298: primersearch.Po: No such file or directory
>>>>> Makefile:2299: printsextract.Po: No such file or directory
>>>>> Makefile:2300: profit.Po: No such file or directory
>>>>> Makefile:2301: prophecy.Po: No such file or directory
>>>>> Makefile:2302: prophet.Po: No such file or directory
>>>>> Makefile:2303: prosextract.Po: No such file or directory
>>>>> Makefile:2304: pscan.Po: No such file or directory
>>>>> Makefile:2305: rebaseextract.Po: No such file or directory
>>>>> Makefile:2306: recoder.Po: No such file or directory
>>>>> Makefile:2307: redata.Po: No such file or directory
>>>>> Makefile:2308: remap.Po: No such file or directory
>>>>> Makefile:2309: restover.Po: No such file or directory
>>>>> Makefile:2310: restrict.Po: No such file or directory
>>>>> Makefile:2311: revseq.Po: No such file or directory
>>>>> Makefile:2312: seealso.Po: No such file or directory
>>>>> Makefile:2313: seqinfo.Po: No such file or directory
>>>>> Makefile:2314: seqmatchall.Po: No such file or directory
>>>>> Makefile:2315: seqret.Po: No such file or directory
>>>>> Makefile:2316: seqretall.Po: No such file or directory
>>>>> Makefile:2317: seqretallfeat.Po: No such file or directory
>>>>> Makefile:2318: seqretset.Po: No such file or directory
>>>>> Makefile:2319: seqretsingle.Po: No such file or directory
>>>>> Makefile:2320: seqretsplit.Po: No such file or directory
>>>>> Makefile:2321: showalign.Po: No such file or directory
>>>>> Makefile:2322: showdb.Po: No such file or directory
>>>>> Makefile:2323: showfeat.Po: No such file or directory
>>>>> Makefile:2324: showorf.Po: No such file or directory
>>>>> Makefile:2325: showseq.Po: No such file or directory
>>>>> Makefile:2326: shuffleseq.Po: No such file or directory
>>>>> Makefile:2327: sigcleave.Po: No such file or directory
>>>>> Makefile:2328: silent.Po: No such file or directory
>>>>> Makefile:2329: sirna.Po: No such file or directory
>>>>> Makefile:2330: sixpack.Po: No such file or directory
>>>>> Makefile:2331: skipseq.Po: No such file or directory
>>>>> Makefile:2332: splitter.Po: No such file or directory
>>>>> Makefile:2333: stretcher.Po: No such file or directory
>>>>> Makefile:2334: stssearch.Po: No such file or directory
>>>>> Makefile:2335: supermatcher.Po: No such file or directory
>>>>> Makefile:2336: syco.Po: No such file or directory
>>>>> Makefile:2337: testplot.Po: No such file or directory
>>>>> Makefile:2338: textsearch.Po: No such file or directory
>>>>> Makefile:2339: tfextract.Po: No such file or directory
>>>>> Makefile:2340: tfm.Po: No such file or directory
>>>>> Makefile:2341: tfscan.Po: No such file or directory
>>>>> Makefile:2342: tmap.Po: No such file or directory
>>>>> Makefile:2343: tranalign.Po: No such file or directory
>>>>> Makefile:2344: transeq.Po: No such file or directory
>>>>> Makefile:2345: treetypedisplay.Po: No such file or directory
>>>>> Makefile:2346: trimest.Po: No such file or directory
>>>>> Makefile:2347: trimseq.Po: No such file or directory
>>>>> Makefile:2348: twofeat.Po: No such file or directory
>>>>> Makefile:2349: union.Po: No such file or directory
>>>>> Makefile:2350: vectorstrip.Po: No such file or directory
>>>>> Makefile:2351: water.Po: No such file or directory
>>>>> Makefile:2352: whichdb.Po: No such file or directory
>>>>> Makefile:2353: wobble.Po: No such file or directory
>>>>> Makefile:2354: wordcount.Po: No such file or directory
>>>>> Makefile:2355: wordmatch.Po: No such file or directory
>>>>> Makefile:2356: wossname.Po: No such file or directory
>>>>> Makefile:2357: yank.Po: No such file or directory
>>>>> make: *** No rule to make target `yank.Po'.  Stop.
>>>>> #
>>>>
>>>>
>>>>
>>>> What am I missing?
>>>>
>>>> Regards,
>>>>
>>>> martin
>>>>
>>>> -- 
>>>> Mart?n Sarachu
>>>> mad at biol.unlp.edu.ar
>>>> EMBNet Argentina
>>>> http://www.ar.embnet.org
>>>
>>>
>>
>> -- 
>> Mart?n Sarachu
>> mad at biol.unlp.edu.ar
>> EMBNet Argentina
>> http://www.ar.embnet.org
> 
> 
> 

-- 
Mart?n Sarachu
mad at biol.unlp.edu.ar
EMBNet Argentina
http://www.ar.embnet.org


From pmr at ebi.ac.uk  Tue Feb 24 14:31:35 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Tue, 24 Feb 2004 14:31:35 +0000
Subject: [EMBOSS] cannot compile a single program
In-Reply-To: <403B5E8A.8000002@biol.unlp.edu.ar>
References: <5.2.1.1.1.20040223145844.00acecd0@udcf.gla.ac.uk> <5.2.1.1.1.20040223145844.00acecd0@udcf.gla.ac.uk> <5.2.1.1.1.20040224135709.0315dd68@udcf.gla.ac.uk> <403B5E8A.8000002@biol.unlp.edu.ar>
Message-ID: <403B6047.80001@ebi.ac.uk>

Mart?n Sarachu wrote:

> Hi
> 
> installed libtool-1.5.2 and yet the same errors
>>>> /bin/sh ../libtool --mode=compile gcc -DPACKAGE_NAME=\"\" 
>>>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
>>>> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2.6.0\" 
>>>> -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 
>>>> -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 
>>>> -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 
>>>> -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 
>>>> -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 
>>>> -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 
>>>> -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 
>>>> -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1  -I. -I. -I/usr/X11R6/include -I./ 
>>>> -I/usr/include/gd    -g -O2 -c -o pdfutils.lo `test -f pdfutils.c || 
>>>> echo './'`pdfutils.c
>>>> ../libtool: s%^.*/%%: No such file or directory
>>>> ../libtool: -e: command not found

The EMBOSS README file suggests:

On some systems there may be compatibility problems with different
automake, autoconf or libtool versions. Always make sure that you keep
up to date with releases of these tools and let us know of any
problems you experience (emboss-bug at embnet.org). If a libtool problem
does arise you can try deleting the following files:

    config.cache
    ltmain.sh
    ltconfig
    libtool

and then type

    aclocal -I m4
    autoconf
    automake -a

and then retry the make.


But I have to wonder whether you are using the CVS version of the code 
... that "-DVERSION=2.6.0" does not look right!!!!!

For the current CVS it is 2.9.0 (although we will be making a 2.8.1 
release soon).

Also, for one-off programs, I plan to add a "myemboss" EMBASSY directory 
to EMBOSS 2.9.0 with instructions for compiling your own local programs.

Hope this helps,

Peter Rice



From mad at biol.unlp.edu.ar  Tue Feb 24 14:45:45 2004
From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=)
Date: Tue, 24 Feb 2004 11:45:45 -0300
Subject: [EMBOSS] cannot compile a single program
In-Reply-To: <403B6047.80001@ebi.ac.uk>
References: <5.2.1.1.1.20040223145844.00acecd0@udcf.gla.ac.uk> <5.2.1.1.1.20040223145844.00acecd0@udcf.gla.ac.uk> <5.2.1.1.1.20040224135709.0315dd68@udcf.gla.ac.uk> <403B5E8A.8000002@biol.unlp.edu.ar> <403B6047.80001@ebi.ac.uk>
Message-ID: <403B6399.5010100@biol.unlp.edu.ar>

CVS version is still downloading... :)

I'm trying to add some programs to our current emboss version (2.6.0) so I'm 
working under the distribution directory of EMBOSS-2.6.0
I've added BLAST and FASTA wrappers without any trouble by adding entries in 
emboss/Makefile.am and doing a 'make blast_wrapper'

Peter Rice wrote:
> Mart?n Sarachu wrote:
> 
>> Hi
>>
>> installed libtool-1.5.2 and yet the same errors
>>
>>>>> /bin/sh ../libtool --mode=compile gcc -DPACKAGE_NAME=\"\" 
>>>>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
>>>>> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2.6.0\" 
>>>>> -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 
>>>>> -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 
>>>>> -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 
>>>>> -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 
>>>>> -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 
>>>>> -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 
>>>>> -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 
>>>>> -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1  -I. -I. -I/usr/X11R6/include -I./ 
>>>>> -I/usr/include/gd    -g -O2 -c -o pdfutils.lo `test -f pdfutils.c 
>>>>> || echo './'`pdfutils.c
>>>>> ../libtool: s%^.*/%%: No such file or directory
>>>>> ../libtool: -e: command not found
> 
> 
> The EMBOSS README file suggests:
> 
> On some systems there may be compatibility problems with different
> automake, autoconf or libtool versions. Always make sure that you keep
> up to date with releases of these tools and let us know of any
> problems you experience (emboss-bug at embnet.org). If a libtool problem
> does arise you can try deleting the following files:
> 
>    config.cache
>    ltmain.sh
>    ltconfig
>    libtool
> 
> and then type
> 
>    aclocal -I m4
>    autoconf
>    automake -a
> 
> and then retry the make.
> 
> 
> But I have to wonder whether you are using the CVS version of the code 
> ... that "-DVERSION=2.6.0" does not look right!!!!!
> 
> For the current CVS it is 2.9.0 (although we will be making a 2.8.1 
> release soon).
> 
> Also, for one-off programs, I plan to add a "myemboss" EMBASSY directory 
> to EMBOSS 2.9.0 with instructions for compiling your own local programs.
> 
> Hope this helps,
> 
> Peter Rice
> 

-- 
Mart?n Sarachu
mad at biol.unlp.edu.ar
EMBNet Argentina
http://www.ar.embnet.org


From a.garcia at imb.uq.edu.au  Wed Feb 25 13:35:27 2004
From: a.garcia at imb.uq.edu.au (a.garcia at imb.uq.edu.au)
Date: Wed, 25 Feb 2004 23:35:27 +1000
Subject: [EMBOSS] pipelines/wflows/PISE
Message-ID: <web-3883384@imb.uq.edu.au>

G-PIPE is a work flow generator for PISE/EMBOSS. It allows 
users to easily define and monitor work flows (in-silicon) 
experiments. Once the work flows have been defined (steps, 
parameters, conditions) users can save them as XML files 
and share them across different GPIPE installations. Users 
can also distribute different works with in a work flow 
across different servers around a grid. 

This is the first official release of GPIPE, we hope to 
improve on a later release. We appreciate your comments. 

The server where GPIPE is in the moment 
(http://sirio.sanmartin.edu.co/Pise/gpipe.html)does not 
allow run complex work flows (computing demanding) but is 
enough  to exemplify GPIPE's capacities. Information is 
also available at 
http://www.pasteur.fr/recherche/unites/sis/Pise/#


From d.m.a.martin at dundee.ac.uk  Wed Feb 25 15:33:09 2004
From: d.m.a.martin at dundee.ac.uk (David Martin)
Date: Wed, 25 Feb 2004 15:33:09 +0000
Subject: [EMBOSS] Adding new programs on OS X - aclocal problem
Message-ID: <BC6270B5.E787%d.m.a.martin@dundee.ac.uk>

I have been trying to add some local code in to EMBOSS on OS X. I have the
latest and greatest autoconf and automake. Iget problems with aclocal as:

% aclocal -I m4
aclocal: couldn't open directory `m4': No such file or directory

and % aclocal
aclocal: configure.in: 140: macro `AM_PROG_LIBTOOL' not found in library

Any suggestions or do I have to do some manual hacking of the various
configure scripts?

..d



From d.m.a.martin at dundee.ac.uk  Wed Feb 25 17:01:21 2004
From: d.m.a.martin at dundee.ac.uk (David Martin)
Date: Wed, 25 Feb 2004 17:01:21 +0000
Subject: [EMBOSS] More OS X woes
Message-ID: <BC628561.E79E%d.m.a.martin@dundee.ac.uk>

OK, I have now tried the cvs version of EMBOSS.

aclocal -I m4 runs without errors

Autoconf fails with:
% autoconf -v
... bits snipped ...
autom4te: creating configure
autom4te: formatting traces for `/tmp/am4txD3aAT/patterns':
m4_pattern_allow, m4_pattern_forbid
autom4te: forbidden tokens: ^_?A[CHUM]_|_AC_|^LIBOBJS$|^_?m4_|^dnl$|^_?AS_
autom4te: forbidden token : ^LIBOBJS$ => do not use LIBOBJS directly, use
AC_LIBOBJ (see section `AC_LIBOBJ vs LIBOBJS'
autom4te: allowed   tokens: ^AM_[A-Z]+FLAGS$|^AS_FLAGS$
configure.in:151: error: possibly undefined macro: AC_PROG_LIBTOOL
      If this token and others are legitimate, please use m4_pattern_allow.
      See the Autoconf documentation.


Any thoughts?

..d



From pmr at ebi.ac.uk  Wed Feb 25 17:10:54 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Wed, 25 Feb 2004 17:10:54 +0000
Subject: [EMBOSS] More OS X woes
In-Reply-To: <BC628561.E79E%d.m.a.martin@dundee.ac.uk>
References: <BC628561.E79E%d.m.a.martin@dundee.ac.uk>
Message-ID: <403CD71E.7030000@ebi.ac.uk>

David Martin wrote:

> OK, I have now tried the cvs version of EMBOSS.
> 
> aclocal -I m4 runs without errors
> 
> Autoconf fails with:
> % autoconf -v
> ... bits snipped ...

> Any thoughts?

autoconf does that for me too ... but without the -v it is perfectly happy.

Followups to emboss-bug, please!

Peter



From jmarken at trubion.com  Fri Feb 27 00:50:39 2004
From: jmarken at trubion.com (John Marken)
Date: Thu, 26 Feb 2004 16:50:39 -0800
Subject: [EMBOSS] jemboss rebase etc can't utilize embossre.enz file
Message-ID: <c98c78e91e13524ca8c66dc7243ef5a0403e9462@genecraft.com>

Hello,
Just installed jemboss, the interface works but programs needing database files like remap don't work. Remap can return the sequence and translations but no restriction enzyme sites are shown, nor are there enzymes listed the cuts or no cut sections of the resulting file. Command line emboss is working and  remap can find the rebase (embossre.enz etc)  files as specified in the .embossrc in //usr/local/emboss/share/EMBOSS/data/REBASE.

The jemboss.properties file in
"//usr/local/jakarta-tomcat-4.1.29/webapps/axis/WEB-INF/classes/resources"
contains the line 
"embossData=/usr/local/emboss/share/EMBOSS/data/" (without quotes)

Is the jemboss.propterties file in the right place? Is there another config file that needs editing?

Regards
John Marken


Trubion Pharmaceuticals Inc.
2401 4th Ave. Suite 1050
Seattle, WA 98121
206-838-0500




From jmarken at trubion.com  Fri Feb 27 19:04:34 2004
From: jmarken at trubion.com (John Marken)
Date: Fri, 27 Feb 2004 11:04:34 -0800
Subject: [EMBOSS] jemboss rebase etc can't utilize embossre.enz file
Message-ID: <24080b25f20f0ebe98ed200caebb3b1d403f94c4@genecraft.com>


Thank you. There indeed was another copy of jemboss.properties in the home directory for the tomcat server owner. And it actually is important to not install  the server as root:>)

John
-----Original Message-----
From: Dr T. Carver [mailto:tcarver at rfcgr.mrc.ac.uk]
Sent: Friday, February 27, 2004 2:25 AM
To: John Marken
Subject: Re: [EMBOSS] jemboss rebase etc can't utilize embossre.enz file


Hi John

This looks to be the correct jemboss.properties (just ensure there isn't
one in the home directory of the tomcat user).

Did you run 'rebaseextract'?

What does the rest of the jemboss.properties look like?

Regards
Tim

Tim Carver
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494500  Fax: +44 1223 494512
E-mail: tcarver at rfcgr.mrc.ac.uk  Web: http://www.rfcgr.mrc.ac.uk


On Thu, 26 Feb 2004, John Marken wrote:

> Hello,
> Just installed jemboss, the interface works but programs needing database files like remap don't work. Remap can return the sequence and translations but no restriction enzyme sites are shown, nor are there enzymes listed the cuts or no cut sections of the resulting file. Command line emboss is working and  remap can find the rebase (embossre.enz etc)  files as specified in the .embossrc in //usr/local/emboss/share/EMBOSS/data/REBASE.
>
> The jemboss.properties file in
> "//usr/local/jakarta-tomcat-4.1.29/webapps/axis/WEB-INF/classes/resources"
> contains the line
> "embossData=/usr/local/emboss/share/EMBOSS/data/" (without quotes)
>
> Is the jemboss.propterties file in the right place? Is there another config file that needs editing?
>
> Regards
> John Marken
>
>
> Trubion Pharmaceuticals Inc.
> 2401 4th Ave. Suite 1050
> Seattle, WA 98121
> 206-838-0500
>
>




From ouse_ser_magro at ig.com.br  Fri Feb 27 19:27:01 2004
From: ouse_ser_magro at ig.com.br (Carujo,,)
Date: Fri, 27 Feb 2004 19:27:01 +0000 (GMT)
Subject: [EMBOSS] RE, respuesta..
Message-ID: <20040227192701.AEDEA7D110@mercury.hgmp.mrc.ac.uk>

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