From charles-listes-emboss at plessy.org  Mon Sep  4 00:28:50 2006
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Mon, 4 Sep 2006 13:28:50 +0900
Subject: [EMBOSS] Manpage generator
Message-ID: <20060904042850.GC14634@kunpuu.plessy.org>

Dear emboss developpers,

I am a member of the Debian-med project, and we intend to provide Debian
packages for EMBOSS soon. First of all, if some persons reading this
mail would be interestd to participae to this effort, we are very open
to collaboration, and we even have dedicated facilities for this:

http://alioth.debian.org/projects/pkg-emboss/

It is part from the Debian policy that any program in the /usr/bin and
sister directories should have a man page, and EMBOSS programs do not
provide them, so I decided that I will develop a manpage generator.

For the moment, I intend to parse the .acd files, fill templates in the
DocBook format, and convert them using an xsl stylesheet. I welcome any
suggestion on how to parse the .acd files for this purpose (I have no
other plan than using brute force with perl).

Have a nice day,

-- 
Charles Plessy
http://charles.plessy.org
Wako, Saitama, Japan


From David.Bauer at schering.de  Mon Sep  4 01:54:01 2006
From: David.Bauer at schering.de (David.Bauer at schering.de)
Date: Mon, 4 Sep 2006 07:54:01 +0200
Subject: [EMBOSS] Antwort:  How to modify a program?
In-Reply-To: <001a01c654d4$6bfc13c0$1b02a8c0@tao>
Message-ID: <OFD521873A.74CBFA77-ONC12571DF.001FD412-C12571DF.00206DC4@schering.de>


Anything in ajax and nucleus is incorporated in the libraries libajax and
libnucleus.
So you must rebuild/reinstall  theses libraries.
Just run a 'make install' in the top emboss source dir and this will
rebuild the modified library and your application.
The make utility looks at the modification time of the files so it will
recompile only those which have been changed.

HTH,
David.

emboss-bounces at lists.open-bio.org schrieb am 31/03/2006 17:04:32:

> Hi,
>
>      I am new to Unix system, so sorry if it is a too simple question.
> I need to modify the DIGEST  program (\EMBOSS-4.0.0\emboss\digest)
> to change some rules for trypsin digestion. The part of the program that
> I need to modify is in another program (EMBOSS-4.0.0\nucleus\embprop.c).
> After modify the embprop program I compiled with gcc and got a embprop.o
> file. But when I ran the DIGEST program it still give the same results
and
> didn't
> change. Are there some steps that I missed?
>
>      Thanks a lot for your help!
>
>      Regards,
>
>      Tao
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss



From David.Bauer at schering.de  Mon Sep  4 02:57:54 2006
From: David.Bauer at schering.de (David.Bauer at schering.de)
Date: Mon, 4 Sep 2006 08:57:54 +0200
Subject: [EMBOSS] Antwort:  Manpage generator
In-Reply-To: <20060904042850.GC14634@kunpuu.plessy.org>
Message-ID: <OFEA4A36A9.0EB51F74-ONC12571DF.00259DD5-C12571DF.00264720@schering.de>


Hi,

there are a kind of manpages in text and html format provided with emboss.
They are installed in
<prefix>/share/EMBOSS/doc/html/emboss/apps
and
<prefix>/share/EMBOSS/doc/programs/text

The txt files are used by the emboss application 'tfm' which displays this
documentation like man does.
The html files are for developers of web interfaces.

If you want to parse ACD files you should have a look at the "emboss
explorer" web gui.
This uses perl modules to parse acd files and create the web interface
dynamically.

HTH,
David.


emboss-bounces at lists.open-bio.org schrieb am 04/09/2006 06:28:50:

> Dear emboss developpers,
>
> I am a member of the Debian-med project, and we intend to provide Debian
> packages for EMBOSS soon. First of all, if some persons reading this
> mail would be interestd to participae to this effort, we are very open
> to collaboration, and we even have dedicated facilities for this:
>
> http://alioth.debian.org/projects/pkg-emboss/
>
> It is part from the Debian policy that any program in the /usr/bin and
> sister directories should have a man page, and EMBOSS programs do not
> provide them, so I decided that I will develop a manpage generator.
>
> For the moment, I intend to parse the .acd files, fill templates in the
> DocBook format, and convert them using an xsl stylesheet. I welcome any
> suggestion on how to parse the .acd files for this purpose (I have no
> other plan than using brute force with perl).
>
> Have a nice day,
>
> --
> Charles Plessy
> http://charles.plessy.org
> Wako, Saitama, Japan
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss



From jison at ebi.ac.uk  Mon Sep  4 09:13:38 2006
From: jison at ebi.ac.uk (Jon Ison)
Date: Mon, 4 Sep 2006 14:13:38 +0100 (BST)
Subject: [EMBOSS] Question about make use of multiple fields indexing by
 dbxfasta or dbxflat
In-Reply-To: <000501c6c6f4$66aad770$be4de780@CIT.NIH.GOV>
References: <000501c6c6f4$66aad770$be4de780@CIT.NIH.GOV>
Message-ID: <34864.172.31.70.94.1157375618.squirrel@webmail.ebi.ac.uk>

Hi Jean

The short answer is, by adding extra fields, all programs that
read sequence(s) would benefit from increased flexibility in
how sequences may be specified on the command-line.

You can read about how to specify sequences using the Uniform
Sequence Address (USA) model here:
http://emboss.sourceforge.net/docs/themes/UniformSequenceAddress.html

(look under "The Full USA syntax")

If any applications absolutely required certain indexing then that
would be mentioned in the application documentation, accessible via:
http://emboss.sourceforge.net/apps/

Cheers

Jon



> Hello,
>
> I need to index swissprot data file from uniprot.org. They have two formats : fasta and flat available. I understand I
> can specify fields to be indexed. And there are more fields can be specified if using flat file with dbxflat. However,
> I am not sure how many programs in EMBOSS package will be benefit from specifying extra fields other than acc and id
> except 'seqret'? Could someone let me know how to find the answer? Thanks you very much in advance.
>
> Jean
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>




From aidanfindlater at gmail.com  Mon Sep  4 10:03:30 2006
From: aidanfindlater at gmail.com (Aidan Findlater)
Date: Mon, 4 Sep 2006 10:03:30 -0400
Subject: [EMBOSS] EMBOSS cai
Message-ID: <bd79799b0609040703x1d525d76oade13ca7763b4fd7@mail.gmail.com>

I'm trying to figure out what the appropriate table for calculating
the CAIs of fission yeast sequences.

The documentation says, "The default codon usage table 'Eyeastcai.cut'
was prepared from a set of S. pombe genes by Peter Rice." If you copy
the example in the documentation (that uses a fission yeast gene with
the Eyeastcai.cut table), you get the same results that they show.

However, if you look at the index of tables in EMBOSS's data
directory, it says that Eyeast_cai.cut is the
"Saccharomyces_cerevisiae original CAI set (Eyeastcai.cut)". The table
that is identified as being fission yeast gives very different
numbers.

Any clarification would be greatly appreciated!

Thanks,

Aidan Findlater


From pmr at ebi.ac.uk  Mon Sep  4 10:46:39 2006
From: pmr at ebi.ac.uk (pmr at ebi.ac.uk)
Date: Mon, 4 Sep 2006 15:46:39 +0100 (BST)
Subject: [EMBOSS] EMBOSS cai
In-Reply-To: <bd79799b0609040703x1d525d76oade13ca7763b4fd7@mail.gmail.com>
References: <bd79799b0609040703x1d525d76oade13ca7763b4fd7@mail.gmail.com>
Message-ID: <2099.82.68.212.94.1157381199.squirrel@webmail.ebi.ac.uk>

Dear Aidan,

> I'm trying to figure out what the appropriate table for calculating
> the CAIs of fission yeast sequences.
>
> The documentation says, "The default codon usage table 'Eyeastcai.cut'
> was prepared from a set of S. pombe genes by Peter Rice." If you copy
> the example in the documentation (that uses a fission yeast gene with
> the Eyeastcai.cut table), you get the same results that they show.

Oops. Confusion (missing line) in the documentation for the cai
application. We have tables for Saccharomyces cerevisiae and
Schizosaccharomyces pombe. Fission yeast is in Eschpo_cai.cut, cerevisiae
is in Eyeast_cai.cut. I will fix the docuemntation.

In previous releases of EMBOSS the names were Epombecai.cut and
Eyeastcai.cut. Release 4.0.0 has both names - future versions will use the
new names to make the species clearer.

I prepared both tables. Eyeast_cai.cut gives the published cerevisiae CAI
values (the tables do not quite match the current gene sequences).
Eschpo_cai.cut uses the same genes from S. pombe and is the one to use for
fission yeast. The tabel was set uip for the pombe sequencers at Sanger.
They may be able to give you more information about how useful the results
are.

Hope that helps,

Peter



From golharam at umdnj.edu  Tue Sep  5 12:39:22 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Tue, 05 Sep 2006 12:39:22 -0400
Subject: [EMBOSS] EMBOSS-Explorer & EMBOSS-4.0.0
Message-ID: <03f201c6d109$d725d710$2f01a8c0@GOLHARMOBILE1>

I recently installed EMBOSS 4 and am encountering the "unknown datatype
pattern"  error for fuzznuc (new to EMBOSS 4).  

Here's the URL:
http://serine.umdnj.edu/cgi-bin/emboss/fuzznuc  

I've been trying to get a hold of Luke but email is bouncing back...

Ryan



From maoj at helix.nih.gov  Tue Sep  5 14:35:25 2006
From: maoj at helix.nih.gov (Jean Mao)
Date: Tue, 5 Sep 2006 14:35:25 -0400
Subject: [EMBOSS] Question regarding seqret
Message-ID: <000001c6d11a$0db13530$be4de780@CIT.NIH.GOV>

Hi, 
I have a question hopefully someone can help me about it.

I downloaded the gbrvt1.seq file from ftp://ftp.ncbi.nih.gov/genbank/ as a test, gunzip and index it with dbxflat (I know it's not > than 2gb):

%  dbxflat -dbname=testdb -dbresource=embl -idformat=gb -directory=. -fields='id,acc,sv,des' -filenames='gbvrt*.seq' -indexoutdir=. -release=0.0 -date='00/00/00'

Then I run 'seqret' but failed to retrieve entries using 'sv' or 'des' fields:

% seqret
Reads and writes (returns) sequences
Input (gapped) sequence(s): testdb-sv:11186
Error: USA 'testdb-sv:11186' query field 'sv' not defined for database 'testdb'
Error: Unable to read sequence 'testdb-sv:11186'
Input (gapped) sequence(s): testdb-des:ribosomal
Error: USA 'testdb-des:ribosomal' query field 'des' not defined for database 'testdb'
Error: Unable to read sequence 'testdb-des:ribosomal'
Died: seqret terminated: Bad value for '-sequence' and no more retries

Even the entry does exist if I retrieve with acc number:

% seqret
Reads and writes (returns) sequences
Input (gapped) sequence(s): testdb:X67626
output sequence(s) [aa12srrna.fasta]: /scratch/out1 
%

I did tried dbiflat on this file but still have no luck with similar results.

Thank you.

Jean



From tao.song at calibrant.com  Tue Sep  5 19:54:24 2006
From: tao.song at calibrant.com (Tao Song)
Date: Tue, 5 Sep 2006 19:54:24 -0400
Subject: [EMBOSS]  protein sequence format question
Message-ID: <002101c6d146$c22442b0$1b02a8c0@tao>

Hi,

      I try to use DIGEST function in EMBOSS for tryptic digest
of protein sequence. The sequence file I download from the following 
link:
ftp://ftp.ebi.ac.uk/pub/databases/biomart/current/uniprot_mart_17/uniprot_sequence__sequence__main.txt.gz 

     It is a tab delimited flat file which includes all protein sequences. It seems
that it is not any of the formats EMBOSS support. I wonder is it still possible
to use DIGEST function?

     I attached a small file of the sequence database.

     Thanks a lot for your help!

     Regards,

     Tao     
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: protein table.txt
Url: http://lists.open-bio.org/pipermail/emboss/attachments/20060905/a50c2348/attachment.txt 

From David.Bauer at SCHERING.DE  Wed Sep  6 01:45:59 2006
From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE)
Date: Wed, 6 Sep 2006 07:45:59 +0200
Subject: [EMBOSS] Antwort:   protein sequence format question
In-Reply-To: <002101c6d146$c22442b0$1b02a8c0@tao>
Message-ID: <OFC6DF417C.78B72017-ONC12571E1.001EEC8F-C12571E1.001FAD1B@schering.de>


Hi,

the file which you try to use is a mysql dump from the biomart database.
So this is not a format which you can use with EMBOSS.
But the uniprot is also available in other formats.
Please have a look at the directory:
ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/

There you will find uniprot in fasta and embl (.dat.gz) format which can
be used with EMBOSS.
You can also index these files with the EMBOSS tools dbxfasta or dbxflat
so you can efficently retrieve individual sequences from the database.

Some more information about the sequence format supported by EMBOSS you
can find at the emboss documentation pages:
http://emboss.sourceforge.net/docs/themes/SequenceFormats.html


HTH,
David.

emboss-bounces at lists.open-bio.org schrieb am 06/09/2006 01:54:24:

> Hi,
>
>       I try to use DIGEST function in EMBOSS for tryptic digest
> of protein sequence. The sequence file I download from the following
> link:
> ftp://ftp.ebi.ac.
>
uk/pub/databases/biomart/current/uniprot_mart_17/uniprot_sequence__sequence__main.

> txt.gz
>
>      It is a tab delimited flat file which includes all protein
> sequences. It seems
> that it is not any of the formats EMBOSS support. I wonder is it
> still possible
> to use DIGEST function?



From imadnansyed at yahoo.com  Wed Sep  6 03:52:59 2006
From: imadnansyed at yahoo.com (Adnan Shahzad)
Date: Wed, 6 Sep 2006 00:52:59 -0700 (PDT)
Subject: [EMBOSS] Installing EMBOSS on SERVER
Message-ID: <20060906075259.2243.qmail@web61225.mail.yahoo.com>

Hello all,
  Well I want to run EMBOSS on my server and I want other client (pc) should access all the programs from their I am having trouble understanding how I can make client interface for the EMBOSS
.i am lost need your help.
  Thank you
  Regards,
   Adnan Shahzad


  Adnan Shahzad Research Officer Department of Bioinformatics National Centre of Excellence in Molecular Biology Lahore, Pakistan.
  web: www.cemb.edu.pk Off:- 042-5423952 Ext. 303 Cell:- 0300-5337765
   


 		
---------------------------------
Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and 30+ countries) for 2?/min or less.


From simon.andrews at bbsrc.ac.uk  Wed Sep  6 04:08:14 2006
From: simon.andrews at bbsrc.ac.uk (Simon Andrews)
Date: Wed, 6 Sep 2006 09:08:14 +0100
Subject: [EMBOSS] Installing EMBOSS on SERVER
In-Reply-To: <20060906075259.2243.qmail@web61225.mail.yahoo.com>
References: <20060906075259.2243.qmail@web61225.mail.yahoo.com>
Message-ID: <41333353-2A41-4B79-B41A-01F3783A52DC@bbsrc.ac.uk>


On 6 Sep 2006, at 08:52, Adnan Shahzad wrote:

> Hello all,
>   Well I want to run EMBOSS on my server and I want other client  
> (pc) should access all the programs from their I am having trouble  
> understanding how I can make client interface for the EMBOSS?.i am  
> lost need your help.

You have a couple of choices.

You could let everyone have an account on your server and let them  
log on to your server to run the programs directly.  Probably the  
most common way to do this would be to provide everyone with an ssh  
client to allow secure access to the server from their PCs.  We use  
putty (http://www.chiark.greenend.org.uk/~sgtatham/putty/), as our  
ssh client, but there are plenty of others.

Alternatively you could install one of the emboss web interfaces and  
a web server on your server and let everyone access the programs via  
a web browser.  Again there are a number of different interfaces  
available.  There's a list of them at http://emboss.sourceforge.net/ 
interfaces/#web.

Hope this helps

Simon.



>   Thank you
>   Regards,
>    Adnan Shahzad
>
>
>   Adnan Shahzad Research Officer Department of Bioinformatics  
> National Centre of Excellence in Molecular Biology Lahore, Pakistan.
>   web: www.cemb.edu.pk Off:- 042-5423952 Ext. 303 Cell:- 0300-5337765
>
>
>
>  		
> ---------------------------------
> Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and  
> 30+ countries) for 2?/min or less.
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss




From tao.song at calibrant.com  Wed Sep  6 09:14:02 2006
From: tao.song at calibrant.com (Tao Song)
Date: Wed, 6 Sep 2006 09:14:02 -0400
Subject: [EMBOSS] Antwort:   protein sequence format question
References: <OFC6DF417C.78B72017-ONC12571E1.001EEC8F-C12571E1.001FAD1B@schering.de>
Message-ID: <001601c6d1b6$5419d530$1b02a8c0@tao>

Hi Divad,

     Thanks so much for your help!

     Regards,

     Tao

----- Original Message ----- 
From: <David.Bauer at SCHERING.DE>
To: "Tao Song" <tao.song at calibrant.com>
Cc: <emboss at lists.open-bio.org>; <emboss-bounces at lists.open-bio.org>
Sent: Wednesday, September 06, 2006 1:45 AM
Subject: Antwort: [EMBOSS] protein sequence format question


>
> Hi,
>
> the file which you try to use is a mysql dump from the biomart database.
> So this is not a format which you can use with EMBOSS.
> But the uniprot is also available in other formats.
> Please have a look at the directory:
> ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/
>
> There you will find uniprot in fasta and embl (.dat.gz) format which can
> be used with EMBOSS.
> You can also index these files with the EMBOSS tools dbxfasta or dbxflat
> so you can efficently retrieve individual sequences from the database.
>
> Some more information about the sequence format supported by EMBOSS you
> can find at the emboss documentation pages:
> http://emboss.sourceforge.net/docs/themes/SequenceFormats.html
>
>
> HTH,
> David.
>
> emboss-bounces at lists.open-bio.org schrieb am 06/09/2006 01:54:24:
>
>> Hi,
>>
>>       I try to use DIGEST function in EMBOSS for tryptic digest
>> of protein sequence. The sequence file I download from the following
>> link:
>> ftp://ftp.ebi.ac.
>>
> uk/pub/databases/biomart/current/uniprot_mart_17/uniprot_sequence__sequence__main.
>
>> txt.gz
>>
>>      It is a tab delimited flat file which includes all protein
>> sequences. It seems
>> that it is not any of the formats EMBOSS support. I wonder is it
>> still possible
>> to use DIGEST function?
>
>
> 



From tao.song at calibrant.com  Wed Sep  6 09:27:52 2006
From: tao.song at calibrant.com (Tao Song)
Date: Wed, 6 Sep 2006 09:27:52 -0400
Subject: [EMBOSS]   protein sequence for individual species
References: <OFC6DF417C.78B72017-ONC12571E1.001EEC8F-C12571E1.001FAD1B@schering.de>
Message-ID: <001b01c6d1b8$4151def0$1b02a8c0@tao>

Hi,

    Is there a place I can download protein sequence file for individual 
species
(such as human, yeast, etc)? or is there a program can parse the big 
sequence file
into small ones for individual species?

     Sorry for so many questin. I am new to bioinformatics.

     Thanks so much for you guys' help!

     Regards,

     Tao 



From bgibbon at email.arizona.edu  Wed Sep  6 11:09:51 2006
From: bgibbon at email.arizona.edu (Bryan Gibbon)
Date: Wed, 6 Sep 2006 08:09:51 -0700
Subject: [EMBOSS] protein sequence for individual species
In-Reply-To: <001b01c6d1b8$4151def0$1b02a8c0@tao>
Message-ID: <CAEDKAEHPDBJLJLCPPAKOEGCCDAA.bgibbon@email.arizona.edu>

This can be easily done from Entrez

http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi

Just use the organism qualifier in the search command. For example to fetch
the sequences for my favorite just enter the command "Zea mays [orgn]". Then
to download the results change the display to the format you want (genbank,
fasta etc.) and use the Send to... File menu command to download the
sequences. For large data sets this can take a while but it is easy.

-----Original Message-----
From: emboss-bounces at lists.open-bio.org
[mailto:emboss-bounces at lists.open-bio.org]On Behalf Of Tao Song
Sent: Wednesday, September 06, 2006 6:28 AM
To: emboss at lists.open-bio.org; emboss-bounces at lists.open-bio.org
Subject: [EMBOSS] protein sequence for individual species


Hi,

    Is there a place I can download protein sequence file for individual
species
(such as human, yeast, etc)? or is there a program can parse the big
sequence file
into small ones for individual species?

     Sorry for so many questin. I am new to bioinformatics.

     Thanks so much for you guys' help!

     Regards,

     Tao

_______________________________________________
EMBOSS mailing list
EMBOSS at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/emboss



From d.gatherer at vir.gla.ac.uk  Thu Sep  7 03:29:19 2006
From: d.gatherer at vir.gla.ac.uk (Derek Gatherer)
Date: Thu, 07 Sep 2006 08:29:19 +0100
Subject: [EMBOSS] protein sequence for individual species
In-Reply-To: <CAEDKAEHPDBJLJLCPPAKOEGCCDAA.bgibbon@email.arizona.edu>
References: <001b01c6d1b8$4151def0$1b02a8c0@tao>
	<CAEDKAEHPDBJLJLCPPAKOEGCCDAA.bgibbon@email.arizona.edu>
Message-ID: <6.2.3.4.1.20060907082703.02ac3e88@lenzie.gla.ac.uk>

For something that has been already curated, try:

http://www.ebi.ac.uk/proteome

Cheers
Derek

At 16:09 06/09/2006, Bryan Gibbon wrote:
>This can be easily done from Entrez
>
>http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi
>
>Just use the organism qualifier in the search command. For example to fetch
>the sequences for my favorite just enter the command "Zea mays [orgn]". Then
>to download the results change the display to the format you want (genbank,
>fasta etc.) and use the Send to... File menu command to download the
>sequences. For large data sets this can take a while but it is easy.
>
>-----Original Message-----
>From: emboss-bounces at lists.open-bio.org
>[mailto:emboss-bounces at lists.open-bio.org]On Behalf Of Tao Song
>Sent: Wednesday, September 06, 2006 6:28 AM
>To: emboss at lists.open-bio.org; emboss-bounces at lists.open-bio.org
>Subject: [EMBOSS] protein sequence for individual species
>
>
>Hi,
>
>     Is there a place I can download protein sequence file for individual
>species
>(such as human, yeast, etc)? or is there a program can parse the big
>sequence file
>into small ones for individual species?
>
>      Sorry for so many questin. I am new to bioinformatics.
>
>      Thanks so much for you guys' help!
>
>      Regards,
>
>      Tao
>
>_______________________________________________
>EMBOSS mailing list
>EMBOSS at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/emboss
>
>_______________________________________________
>EMBOSS mailing list
>EMBOSS at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/emboss



From tao.song at calibrant.com  Thu Sep  7 18:27:22 2006
From: tao.song at calibrant.com (Tao Song)
Date: Thu, 7 Sep 2006 18:27:22 -0400
Subject: [EMBOSS]    iep program for multiple protein sequences
References: <CAEDKAEHPDBJLJLCPPAKOEGCCDAA.bgibbon@email.arizona.edu>
Message-ID: <002b01c6d2cc$cb4fe510$1b02a8c0@tao>

Hi,

     I wonder can the iep program  that calculates the isoelectric point of 
a protein be used
for a protein database? When asked to input protein sequence I gave 'tsw' 
instead of
'tsw:laci_ecoli' I got an error that said 'sequence must be protein sequence 
without BZ U X
or *: found bad character Z'. Does iep can only take one protein sequence as 
input file?

    I really appreciate all the help I got from you guys. Thanks a lot!

     Regards,

     Tao




From David.Bauer at SCHERING.DE  Fri Sep  8 02:28:54 2006
From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE)
Date: Fri, 8 Sep 2006 08:28:54 +0200
Subject: [EMBOSS] Antwort:     iep program for multiple protein sequences
In-Reply-To: <002b01c6d2cc$cb4fe510$1b02a8c0@tao>
Message-ID: <OF7B37072F.87038447-ONC12571E3.0022FEEC-C12571E3.00239B22@schering.de>


Hi Tao,

If you want to specify a whole database as input for iep you must use
iep tsw:\*
or
iep "tsw:*"
If you just say tsw, emboss looks for a file named tsw in the local
directory.

HTH,
David.

emboss-bounces at lists.open-bio.org schrieb am 08/09/2006 00:27:22:

> Hi,
>
>      I wonder can the iep program  that calculates the isoelectric point
of
> a protein be used
> for a protein database? When asked to input protein sequence I gave
'tsw'
> instead of
> 'tsw:laci_ecoli' I got an error that said 'sequence must be protein
sequence
> without BZ U X
> or *: found bad character Z'. Does iep can only take one protein
sequence as
> input file?
>
>     I really appreciate all the help I got from you guys. Thanks a lot!
>
>      Regards,
>
>      Tao
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss



From gbottu at ben.vub.ac.be  Fri Sep  8 03:46:32 2006
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Fri, 8 Sep 2006 09:46:32 +0200
Subject: [EMBOSS] iep program for multiple protein sequences - Checked by
In-Reply-To: <002b01c6d2cc$cb4fe510$1b02a8c0@tao>
References: <CAEDKAEHPDBJLJLCPPAKOEGCCDAA.bgibbon@email.arizona.edu>
	<002b01c6d2cc$cb4fe510$1b02a8c0@tao>
Message-ID: <20060908074632.GA22405@bigben.ulb.ac.be>

On Thu, Sep 07, 2006 at 06:27:22PM -0400, Tao Song wrote:
> I wonder can the iep program  that calculates the isoelectric point of 
> a protein be used
> for a protein database?

Yes, iep can take multiple proteins as input. It will create an output 
file with the titration curves of the different proteins the one after 
the other. It does not make one graph for all the proteins together, 
which would anyway not make much biological sence.

> When asked to input protein sequence I gave 'tsw' 
> instead of
> 'tsw:laci_ecoli' I got an error that said 'sequence must be protein sequence 
> without BZ U X
> or *: found bad character Z'. Does iep can only take one protein sequence as 
> input file?

The problem here is that iep takes as input only a protein sequence 
without ambiguity symbols. The reason is without doubt that it is not 
clear whether B should be handled as a Asp (negative) or a Asn (neutral), 
etc.

	Guy Bottu,
	Belgian EMBnet Node



From pmr at ebi.ac.uk  Fri Sep  8 07:20:24 2006
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 08 Sep 2006 12:20:24 +0100
Subject: [EMBOSS] iep program for multiple protein sequences
In-Reply-To: <002b01c6d2cc$cb4fe510$1b02a8c0@tao>
References: <CAEDKAEHPDBJLJLCPPAKOEGCCDAA.bgibbon@email.arizona.edu>
	<002b01c6d2cc$cb4fe510$1b02a8c0@tao>
Message-ID: <450151F8.5060403@ebi.ac.uk>

Tao Song wrote:
> Hi,
> 
>      I wonder can the iep program  that calculates the isoelectric point of 
> a protein be used
> for a protein database? When asked to input protein sequence I gave 'tsw' 
> instead of
> 'tsw:laci_ecoli' I got an error that said 'sequence must be protein sequence 
> without BZ U X
> or *: found bad character Z'. Does iep can only take one protein sequence as 
> input file?

Your command does read the test swissprot database, but fails on an 
entry that is a sequence fragment with a Z ambiguity code.

For the next release, I have a patch that will convert B and Z to D/N 
and E/Q using the Dayhoff frequencies of naturally occurring amino 
acids. This will convert the first B or Z to a charged residue (as these 
are more common), the second to an uncharged residue, and so on. With 
this change in place iep can be modified to accept any protein sequence 
and will produce consistent results on ambiguity codes.

A question: We can try this fix as a general solution for programs 
requiring "pureprotein" input, by converting any B or Z (or J) ambiguity 
code. Is this useful? For iep the order does not matter and the 
converted sequence does not appear in the output, but I think a 
program-by-program solution is better.

Other programs insisting on "pureprotein" input are hmoment, octanol and 
pepwindow

regards,

Peter


From imadnansyed at yahoo.com  Mon Sep 11 01:43:42 2006
From: imadnansyed at yahoo.com (Adnan Shahzad)
Date: Sun, 10 Sep 2006 22:43:42 -0700 (PDT)
Subject: [EMBOSS] EMBOSS running on server (problems)
Message-ID: <20060911054342.80134.qmail@web61220.mail.yahoo.com>

Hello Every body,
  Need your help and guidance.
  I have tried installing EMBOSS on my server with Wemboss web interface and with Apache server tomcat 5.5 but system seem to be not integrated with each other and things are not running properly.
  Kindly any one tell me any other way to keep it running which is more simpler then this one 
what about running Jemboss. 
  Can some one give me manual for step by step procedure because I am new to all this so I am doing on hit and trail bases.
  And now looking for the help from you guys.
  regards,
   


  Adnan Shahzad Research Officer Department of Bioinformatics National Centre of Excellence in Molecular Biology Lahore, Pakistan.
  web: www.cemb.edu.pk Off:- 042-5423952 Ext. 303 Cell:- 0300-5337765
   


 		
---------------------------------
 All-new Yahoo! Mail - Fire up a more powerful email and get things done faster.


From jison at ebi.ac.uk  Mon Sep 11 04:04:51 2006
From: jison at ebi.ac.uk (Jon Ison)
Date: Mon, 11 Sep 2006 09:04:51 +0100 (BST)
Subject: [EMBOSS] EMBOSS running on server (problems)
In-Reply-To: <20060911054342.80134.qmail@web61220.mail.yahoo.com>
References: <20060911054342.80134.qmail@web61220.mail.yahoo.com>
Message-ID: <1345.84.92.187.247.1157961891.squirrel@webmail.ebi.ac.uk>

Hi Adnan

For people on the list to be able to help, please be much more specific
about details of your system, what you are trying to achieve and the
problems you are having.

In the meantime, if you want a really easy way to run EMBOSS applications,
you can use one of the on-line EMBOSS Explorer (or other) servers listed here:

http://emboss.sourceforge.net/servers/

Cheers

Jon




> Hello Every body,
>   Need your help and guidance.
>   I have tried installing EMBOSS on my server with Wemboss web interface and with Apache server tomcat 5.5 but system
> seem to be not integrated with each other and things are not running properly.
>   Kindly any one tell me any other way to keep it running which is more simpler then this one 
what about running
> Jemboss.
>   Can some one give me manual for step by step procedure because I am new to all this so I am doing on hit and trail
> bases.
>   And now looking for the help from you guys.
>   regards,
>
>
>
>   Adnan Shahzad Research Officer Department of Bioinformatics National Centre of Excellence in Molecular Biology
> Lahore, Pakistan.
>   web: www.cemb.edu.pk Off:- 042-5423952 Ext. 303 Cell:- 0300-5337765
>
>
>
>
> ---------------------------------
>  All-new Yahoo! Mail - Fire up a more powerful email and get things done faster.
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>
>




From golharam at umdnj.edu  Mon Sep 11 12:28:30 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Mon, 11 Sep 2006 12:28:30 -0400
Subject: [EMBOSS] EMBOSS-Explorer Follow-up
Message-ID: <007501c6d5bf$51f63e80$2f01a8c0@GOLHARMOBILE1>

So I stepped through the code for tfm and it looks like it initially
looks in /usr/share/EMBOSS/doc/programs/html.  So 'make install' is
putting the html docs in /usr/share/EMBOSS/doc/html/emboss/apps/...  But
why?  Was this an inadvertant change?


> -----Original Message-----
> From: Ryan Golhar [mailto:golharam at umdnj.edu] 
> Sent: Monday, September 11, 2006 11:38 AM
> To: 'emboss at emboss.open-bio.org'
> Subject: EMBOSS-Explorer
> 
> 
> Does anyone know how to get a hold of Luke McCarthy?  The 
> email address I have for him is getting bounced back and he 
> hasn't responded to his sourceforge email.
> 
> Since I'm on the topic...I have two problems with 
> EMBOSS-Explorer and EMBOSS 4.0.0:
> 
> 1.  EMBOSS-Explorer uses the path of 
> /usr/share/EMBOSS/doc/programs/html, however EMBOSS html docs 
> are installed in /usr/share/EMBOSS/doc/html/emboss.  The 
> EMBASSY docs are in /usr/share/EMBOSS/doc/html/embassy.  
> 
> This seems to be completely different than where the text 
> documents are installed, /usr/share/EMBOSS/doc/programs/txt.  
> It looks like EMBOSS v3 was installing the html docs in 
> /usr/share/EMBOSS/doc/programs/html, but that has changed in v4.
> 
> So, either the EMBOSS installation needs to be told to 
> install in /usr/share/EMBOSS/doc/programs/html, or 
> EMBOSS-Explorer needs to be updated to look in 2 different 
> directories, one for EMBOSS and one for EMBASSY.
> 
> As a third option, EMBOSS-Explorer could run 'tfm -html' to 
> get the html doc generated on the fly.  This is probably 
> overkill though.
> 
> 2.  The new programs introduce new datatypes in the ACD files 
> that EMBOSS-Explorer doesn't recognize.  I get an 'unknown 
> data type' message display in my browser for these apps.
> 
> 
> --
> Ryan Golhar  -  golharam at umdnj.edu
> The Informatics Institute of UMDNJ
> 



From golharam at umdnj.edu  Mon Sep 11 11:37:39 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Mon, 11 Sep 2006 11:37:39 -0400
Subject: [EMBOSS] EMBOSS-Explorer
Message-ID: <006a01c6d5b8$372e7c90$2f01a8c0@GOLHARMOBILE1>

Does anyone know how to get a hold of Luke McCarthy?  The email address
I have for him is getting bounced back and he hasn't responded to his
sourceforge email.

Since I'm on the topic...I have two problems with EMBOSS-Explorer and
EMBOSS 4.0.0:

1.  EMBOSS-Explorer uses the path of
/usr/share/EMBOSS/doc/programs/html, however EMBOSS html docs are
installed in /usr/share/EMBOSS/doc/html/emboss.  The EMBASSY docs are in
/usr/share/EMBOSS/doc/html/embassy.  

This seems to be completely different than where the text documents are
installed, /usr/share/EMBOSS/doc/programs/txt.  It looks like EMBOSS v3
was installing the html docs in /usr/share/EMBOSS/doc/programs/html, but
that has changed in v4.

So, either the EMBOSS installation needs to be told to install in
/usr/share/EMBOSS/doc/programs/html, or EMBOSS-Explorer needs to be
updated to look in 2 different directories, one for EMBOSS and one for
EMBASSY.

As a third option, EMBOSS-Explorer could run 'tfm -html' to get the html
doc generated on the fly.  This is probably overkill though.

2.  The new programs introduce new datatypes in the ACD files that
EMBOSS-Explorer doesn't recognize.  I get an 'unknown data type' message
display in my browser for these apps.


--
Ryan Golhar  -  golharam at umdnj.edu
The Informatics Institute of UMDNJ



From pmr at ebi.ac.uk  Mon Sep 11 13:01:51 2006
From: pmr at ebi.ac.uk (Peter Rice)
Date: Mon, 11 Sep 2006 18:01:51 +0100
Subject: [EMBOSS] EMBOSS-Explorer Follow-up
In-Reply-To: <007501c6d5bf$51f63e80$2f01a8c0@GOLHARMOBILE1>
References: <007501c6d5bf$51f63e80$2f01a8c0@GOLHARMOBILE1>
Message-ID: <4505967F.7030200@ebi.ac.uk>

Ryan Golhar wrote:
> So I stepped through the code for tfm and it looks like it initially
> looks in /usr/share/EMBOSS/doc/programs/html.  So 'make install' is
> putting the html docs in /usr/share/EMBOSS/doc/html/emboss/apps/...  But
> why?  Was this an inadvertant change?

Oops. usr/share/EMBOSS/doc/html/emboss/apps/ is the new location in 
4.0.0 (so we do not have to keep copies of all the EMBASSY application 
documentation in the EMBOSS source).

Will be fixed in 4.0.0. A simple copy is one way to fix it. I will make 
a fix for tfm.

regards,

Peter


From pmr at ebi.ac.uk  Mon Sep 11 13:15:09 2006
From: pmr at ebi.ac.uk (Peter Rice)
Date: Mon, 11 Sep 2006 18:15:09 +0100
Subject: [EMBOSS] EMBOSS-Explorer Follow-up
In-Reply-To: <007501c6d5bf$51f63e80$2f01a8c0@GOLHARMOBILE1>
References: <007501c6d5bf$51f63e80$2f01a8c0@GOLHARMOBILE1>
Message-ID: <4505999D.702@ebi.ac.uk>

Ryan Golhar wrote:
> So I stepped through the code for tfm and it looks like it initially
> looks in /usr/share/EMBOSS/doc/programs/html.  So 'make install' is
> putting the html docs in /usr/share/EMBOSS/doc/html/emboss/apps/...  But
> why?  Was this an inadvertant change?

Aha ... tfm works, but tfm -html may fail.

If the program fails to find the html file, it will check the original 
distribution directory. Unfortunately, if it does find an html file ... 
it may be from version 3. I forgot about the tfm -html option when we 
moved the files.

A fix will take a few days to test. EMBASSY html documentation is not 
under the embassy package, so TFM will have to check the ACD file to 
find the EMBASSY package name. Easy enough - several other programs do 
it - but needs quite a few tests to make sure it does it correctly in 
all cases.

regards,

Peter


From andrespinzon at gmail.com  Mon Sep 11 13:05:33 2006
From: andrespinzon at gmail.com (Andres Pinzon)
Date: Mon, 11 Sep 2006 12:05:33 -0500
Subject: [EMBOSS] Fwd:  EMBOSS running on server (problems)
In-Reply-To: <8968fc7e0609111005s5eca25bbk7b4eb0bb182b67e@mail.gmail.com>
References: <20060911054342.80134.qmail@web61220.mail.yahoo.com>
	<8968fc7e0609111005s5eca25bbk7b4eb0bb182b67e@mail.gmail.com>
Message-ID: <8968fc7e0609111005y5d17c462pce98ccd3477394b5@mail.gmail.com>

---------- Forwarded message ----------
From: Andres Pinzon <andrespinzon at gmail.com>
Date: Sep 11, 2006 12:05 PM
Subject: Re: [EMBOSS] EMBOSS running on server (problems)
To: Adnan Shahzad <imadnansyed at yahoo.com>


On 9/11/06, Adnan Shahzad <imadnansyed at yahoo.com> wrote:
> Hello Every body,
>   Need your help and guidance.
>   I have tried installing EMBOSS on my server with Wemboss web interface and with Apache server tomcat 5.5 but system seem to be not integrated with each other and things are not running properly.

Hmmm... im not sure about this, but maybe it would be better if you
install wEMBOSS on an APACHE "alone" server (not tomcat). At least I
have installed wEMBOSS a couple of times without any problem.
http://bioinf.ibun.unal.edu.co/wEMBOSS/

>   Kindly any one tell me any other way to keep it running which is more simpler then this one ?what about running Jemboss.

You can run jemboss, but as a local installation and it wont be
available on internet or whatever local network you have.

>   Can some one give me manual for step by step procedure because I am new to all this so I am doing on hit and trail bases.

It depends on what interface you are willing to install. If this is
your first time, and you really need a web interface, maybe you should
try EMBOSS explorer, is pretty easy to install, BUT it lacks some good
advantages of wEMBOSS.

>   And now looking for the help from you guys.

;-)
--
Andr?s Pinz?n cPh.D.
[http://www.andrespinzon.com]
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768


-- 
Andr?s Pinz?n cPh.D.
[http://www.andrespinzon.com]
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768



From andrespinzon at gmail.com  Mon Sep 11 13:22:32 2006
From: andrespinzon at gmail.com (Andres Pinzon)
Date: Mon, 11 Sep 2006 12:22:32 -0500
Subject: [EMBOSS] EMBOSS-Explorer
In-Reply-To: <007701c6d5c7$1379dec0$2f01a8c0@GOLHARMOBILE1>
References: <8968fc7e0609111008u1fb383edo11e0bc3719acc699@mail.gmail.com>
	<007701c6d5c7$1379dec0$2f01a8c0@GOLHARMOBILE1>
Message-ID: <8968fc7e0609111022t6d8f0691ub54d2b7e2d38c8a9@mail.gmail.com>

On 9/11/06, Ryan Golhar <golharam at umdnj.edu> wrote:
> But that doesn't help EMBASSY packages
yep, you are right I just noticed it . Excuse me. ;-)
>
> > -----Original Message-----
> > From: Andres Pinzon [mailto:andrespinzon at gmail.com]
> > Sent: Monday, September 11, 2006 1:08 PM
> > To: golharam at umdnj.edu
> > Subject: Re: [EMBOSS] EMBOSS-Explorer
> >
> >
> > On 9/11/06, Ryan Golhar <golharam at umdnj.edu> wrote:
> > > Does anyone know how to get a hold of Luke McCarthy?  The email
> > > address I have for him is getting bounced back and he
> > hasn't responded
> > > to his sourceforge email.
> > >
> > > Since I'm on the topic...I have two problems with
> > EMBOSS-Explorer and
> > > EMBOSS 4.0.0:
> > >
> > > 1.  EMBOSS-Explorer uses the path of
> > > /usr/share/EMBOSS/doc/programs/html, however EMBOSS html docs are
> > > installed in /usr/share/EMBOSS/doc/html/emboss.  The
> > EMBASSY docs are
> > > in /usr/share/EMBOSS/doc/html/embassy.
> >
> > Just make a symlink. It works for me ;-) check it out:
> > http://bioinf.ibun.unal.edu.co/eexplorer/
> > --
> > Andr?s Pinz?n
> > cPh.D.
> > [http://www.andrespinzon.com]
> > Bioinformatics Center, Colombia EMBnet node
> > http://bioinf.ibun.unal.edu.co Tel +57 3165000 > ext 16961 Fax
> > +571 3165415 Micology and Phytopathology Laboratory - Los
> > Andes University. Tel +571 3394949 ext. 2768
> >
>
>


-- 
Andr?s Pinz?n cPh.D.
[http://www.andrespinzon.com]
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768



From andrespinzon at gmail.com  Mon Sep 11 13:08:21 2006
From: andrespinzon at gmail.com (Andres Pinzon)
Date: Mon, 11 Sep 2006 12:08:21 -0500
Subject: [EMBOSS] Fwd:  EMBOSS-Explorer
In-Reply-To: <8968fc7e0609111008u1fb383edo11e0bc3719acc699@mail.gmail.com>
References: <006a01c6d5b8$372e7c90$2f01a8c0@GOLHARMOBILE1>
	<8968fc7e0609111008u1fb383edo11e0bc3719acc699@mail.gmail.com>
Message-ID: <8968fc7e0609111008k496447f0o7f40a2d2002be8b2@mail.gmail.com>

---------- Forwarded message ----------
From: Andres Pinzon <andrespinzon at gmail.com>
Date: Sep 11, 2006 12:08 PM
Subject: Re: [EMBOSS] EMBOSS-Explorer
To: golharam at umdnj.edu


On 9/11/06, Ryan Golhar <golharam at umdnj.edu> wrote:
> Does anyone know how to get a hold of Luke McCarthy?  The email address
> I have for him is getting bounced back and he hasn't responded to his
> sourceforge email.
>
> Since I'm on the topic...I have two problems with EMBOSS-Explorer and
> EMBOSS 4.0.0:
>
> 1.  EMBOSS-Explorer uses the path of
> /usr/share/EMBOSS/doc/programs/html, however EMBOSS html docs are
> installed in /usr/share/EMBOSS/doc/html/emboss.  The EMBASSY docs are in
> /usr/share/EMBOSS/doc/html/embassy.

Just make a symlink. It works for me ;-) check it out:
http://bioinf.ibun.unal.edu.co/eexplorer/
--
Andr?s Pinz?n cPh.D.
[http://www.andrespinzon.com]
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768


-- 
Andr?s Pinz?n cPh.D.
[http://www.andrespinzon.com]
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768



From golharam at umdnj.edu  Mon Sep 11 13:11:35 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Mon, 11 Sep 2006 13:11:35 -0400
Subject: [EMBOSS] EMBOSS-Explorer Follow-up
In-Reply-To: <4505967F.7030200@ebi.ac.uk>
Message-ID: <007601c6d5c5$56589f80$2f01a8c0@GOLHARMOBILE1>

Okay thanks.  Then I think maybe EMBOSS-Explorer should do a 'tfm -html
<appname>'.  That would make it independent of the EMBOSS version and
rely on tfm to generate the html documentation.  I'll play around with
that change.  Do you know how to get a hold of Luke btw?

Ryan


> -----Original Message-----
> From: Peter Rice [mailto:pmr at ebi.ac.uk] 
> Sent: Monday, September 11, 2006 1:02 PM
> To: golharam at umdnj.edu
> Cc: emboss at emboss.open-bio.org
> Subject: Re: [EMBOSS] EMBOSS-Explorer Follow-up
> 
> 
> Ryan Golhar wrote:
> > So I stepped through the code for tfm and it looks like it 
> initially 
> > looks in /usr/share/EMBOSS/doc/programs/html.  So 'make install' is 
> > putting the html docs in 
> /usr/share/EMBOSS/doc/html/emboss/apps/...  
> > But why?  Was this an inadvertant change?
> 
> Oops. usr/share/EMBOSS/doc/html/emboss/apps/ is the new location in 
> 4.0.0 (so we do not have to keep copies of all the EMBASSY 
> application 
> documentation in the EMBOSS source).
> 
> Will be fixed in 4.0.0. A simple copy is one way to fix it. I 
> will make 
> a fix for tfm.
> 
> regards,
> 
> Peter
> 



From golharam at umdnj.edu  Mon Sep 11 14:37:53 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Mon, 11 Sep 2006 14:37:53 -0400
Subject: [EMBOSS] EMBOSS-Explorer Follow-up
In-Reply-To: <416B9A34D7CA1C4C9ED58354E75101BBA3815B@NIHCESMLBX3.nih.gov>
Message-ID: <007b01c6d5d1$653d38b0$2f01a8c0@GOLHARMOBILE1>

Yes, I tried that, but it doesn't work for EMBASSY applications as they
fall in /usr/share/EMBOSS/doc/html/embassy/apps/...

> -----Original Message-----
> From: Mao, Jean (NIH/CIT) [E] [mailto:maoj at mail.nih.gov] 
> Sent: Monday, September 11, 2006 2:28 PM
> To: golharam at umdnj.edu
> Cc: emboss at emboss.open-bio.org
> Subject: RE: [EMBOSS] EMBOSS-Explorer Follow-up
> 
> 
> Have you tried to modify the Conf.pm page? It's under our 
> /usr/local/perl-5.8.7/lib/site_perl/5.8.7/EMBOSS/GUI/Conf.pm 
> and just modify the line to the right directory for the 
> manual html pages. I did and it worked. Luke's email is  
> 'mccarthy at users.sourceforge.net'
> 
> -----Original Message-----
> From: Ryan Golhar [mailto:golharam at umdnj.edu] 
> Sent: Monday, September 11, 2006 1:12 PM
> To: 'Peter Rice'
> Cc: emboss at emboss.open-bio.org
> Subject: Re: [EMBOSS] EMBOSS-Explorer Follow-up
> 
> Okay thanks.  Then I think maybe EMBOSS-Explorer should do a 
> 'tfm -html <appname>'.  That would make it independent of the 
> EMBOSS version and rely on tfm to generate the html 
> documentation.  I'll play around with that change.  Do you 
> know how to get a hold of Luke btw?
> 
> Ryan
> 
> 
> > -----Original Message-----
> > From: Peter Rice [mailto:pmr at ebi.ac.uk]
> > Sent: Monday, September 11, 2006 1:02 PM
> > To: golharam at umdnj.edu
> > Cc: emboss at emboss.open-bio.org
> > Subject: Re: [EMBOSS] EMBOSS-Explorer Follow-up
> > 
> > 
> > Ryan Golhar wrote:
> > > So I stepped through the code for tfm and it looks like it
> > initially
> > > looks in /usr/share/EMBOSS/doc/programs/html.  So 'make 
> install' is
> > > putting the html docs in
> > /usr/share/EMBOSS/doc/html/emboss/apps/...
> > > But why?  Was this an inadvertant change?
> > 
> > Oops. usr/share/EMBOSS/doc/html/emboss/apps/ is the new location in
> > 4.0.0 (so we do not have to keep copies of all the EMBASSY 
> application 
> > documentation in the EMBOSS source).
> > 
> > Will be fixed in 4.0.0. A simple copy is one way to fix it. I will
> > make a fix for tfm.
> > 
> > regards,
> > 
> > Peter
> > 
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org 
> http://lists.open-> bio.org/mailman/listinfo/emboss
> 



From andrespinzon at gmail.com  Tue Sep 12 10:31:08 2006
From: andrespinzon at gmail.com (Andres Pinzon)
Date: Tue, 12 Sep 2006 09:31:08 -0500
Subject: [EMBOSS] EMBOSS running on server (problems)
In-Reply-To: <20060912045707.53921.qmail@web61222.mail.yahoo.com>
References: <8968fc7e0609111005y5d17c462pce98ccd3477394b5@mail.gmail.com>
	<20060912045707.53921.qmail@web61222.mail.yahoo.com>
Message-ID: <8968fc7e0609120731sdc10dd7k7dc86b7bb185aad6@mail.gmail.com>

On 9/11/06, Adnan Shahzad <imadnansyed at yahoo.com> wrote:
>
>
> Hello Andres\
Hi Adnan! Im replying to you as well as to the whole list, maybe this
thread could be helpful for someone, sometime.

> For installing this I need following things right
>
> 1)       EMBOSS
> 2)       Web Server
> 3)       WEMBOSS
> Right

Yep, thats it.

> So when u installed the wemboss you took guidline from its "read me file" or
> you have to use some modification because I am getting some directory error
> for this that is

Yep, I just used that file.

>
> the location of /cgi_bin/ in the file system. I have added the appropriate
> entry in httpd.conf file as said in README file.
> But the server still responds a file not found ERROR.

Ok, by default cgi-bin is a directory above the webroot on your apache
installation.

>
> What should be the location of   /wEMBOSS_cgi/ in the hierarchy of the
> server?

What I did was not to use the apache's cgi-bin default directory but a
wEMBOSS_cgi:  /whatever/wEMBOSS/cgi-bin  and defined this directory as
executable in the httpd.conf file.
It should look like this:
##########################################
ScriptAlias /wEMBOSS_cgi/    "/whatever/wEMBOSS/cgi-bin"

<Directory "/whatever/wEMBOSS/cgi-bin">
Authtype basic
AuthUserFile "/etc/shadow"
require valid-user
Order allow,deny
</directory>
Allow from all
###############################

Please take into account that AuthUserFile can have different methods,
this is just an example, but it should work. In this case what you are
telling to the system is that wemboss will be accesed only for those
users that are valid system users too.
>
> Operating system that I am using is  Linux.

GNU/Linux... cool!

Hope this helps.
-- 
Andr?s Pinz?n cPh.D.
[http://www.andrespinzon.com]
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768



From imadnansyed at yahoo.com  Wed Sep 13 01:59:35 2006
From: imadnansyed at yahoo.com (Adnan Shahzad)
Date: Tue, 12 Sep 2006 22:59:35 -0700 (PDT)
Subject: [EMBOSS] EMBOSS running on server (problems)
In-Reply-To: <20060911160341.GA3050@bigben.ulb.ac.be>
Message-ID: <20060913055935.44143.qmail@web61211.mail.yahoo.com>

Hello Guy Bottu,
  i have cheacked and corrected and now i am getting this error when i run the Wemboss that is 
  " Sorry the owner of the this process is not allowed to run the catch program ask wemboss manager"
   
  i am login and using as admin.
  Kindly need your wise thoughts on it.
   
  Regards
   
  

Guy Bottu <gbottu at ben.vub.ac.be> wrote:
  On Mon, Sep 11, 2006 at 02:02:49AM -0700, Adnan Shahzad wrote:
> My problem is that , 
> the location of /cgi_bin/ in the file system. I have added the appropriate entry in httpd.conf file as said in README file.
> But the server still responds a file not found ERROR.
> 
> What should be the location of /wEMBOSS_cgi/ in the hierarchy of the server?
> 

Your file httpd.conf should contain something as :


ScriptAlias /wEMBOSS_cgi/ /XXX/wEMBOSS/cgi-bin/


AllowOverride None
Options +ExecCGI -Includes
Order allow,deny
Allow from all
AuthType basic
AuthUserFile "/etc/shadow"
Authname 'YYY'
require valid-user



where /XXX/wEMBOSS/cgi-bin is a directory containing catch and emboss.pl.
Note that catch must be setuid :
-rwsr-xr-x 1 root root 12941 2006-09-02 10:47 catch

Instead of /etc/shadow you can have /etc/passwd or whatever file contains 
the user passwords

YYY is a name of a categrory of users (e.g. EMBOSS user) ; it ca, be 
shared with other applications protected by password.

Does that correspond to what you have ?

Guy





  Adnan Shahzad Research Officer Department of Bioinformatics National Centre of Excellence in Molecular Biology Lahore, Pakistan.
  web: www.cemb.edu.pk Off:- 042-5423952 Ext. 303 Cell:- 0300-5337765
   


 		
---------------------------------
 All-new Yahoo! Mail - Fire up a more powerful email and get things done faster.


From neil.brookes at cancer.org.uk  Wed Sep 13 06:19:30 2006
From: neil.brookes at cancer.org.uk (Neil Brookes)
Date: Wed, 13 Sep 2006 11:19:30 +0100
Subject: [EMBOSS] Jemboss problems with fuzzpro and fuzznuc
Message-ID: <4507DB32.7040903@cancer.org.uk>

Hi,

I think I have unearthed an issue with fuzzpro/fuzznuz and EMBOSS 4.0.0
The old version in 3.0.0 had a '-mismatch' option. This has changed in 
version 4.0.0 to '-pmismatch'.

The 'mismatch' integer element seems to have been removed from the 
fuzzpro/nuc ACD files.
I'm not sure how/when Jemboss parses the ACD flies, but it doesn't seem 
to be allowing for the  new '-pmismatch' option, and users are unable to 
specify a value.

any ideas ?

cheers
Neil

-- 
Neil Brookes
Bioinformatics
Cancer Research UK

+ 44 (0)207 2693063



From charles-listes-emboss at plessy.org  Thu Sep 14 11:07:36 2006
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Fri, 15 Sep 2006 00:07:36 +0900
Subject: [EMBOSS] Building EMBOSS with an external libpcre.
Message-ID: <20060914150736.GD1510@kunpuu.plessy.org>

Dear developpers,

I am preparing Debian packages for EMBOSS, and I run in the following
problem:

EMBOSS is shipped and built with its own copy of libpcre. As a result,
the EMBOSS Debian package contains some files wich are also in the
libpcre Debian package, and they conflict together.

I could remove the conflicting files from the EMBOSS package, but I
think that it is unwise, as the libpcre in Debian does not have the same
version number.

It would be much cleaner if I could build EMBOSS with the libpcre from
Debian, but I could not figure out how to do. Can somebody give me
hints?

Have a nice day,

-- 
Charles Plessy
Debian-Med packaging team
http://www.debian.org/devel/debian-med/


From Suraj.Mukatira at STJUDE.ORG  Thu Sep 14 12:14:17 2006
From: Suraj.Mukatira at STJUDE.ORG (Mukatira, Suraj)
Date: Thu, 14 Sep 2006 11:14:17 -0500
Subject: [EMBOSS] installing EMBOSS-4.0.0 in ubuntu
Message-ID: <F2235647AC878D438F09255C39842FBC1563A319@SJMEMXMB03.stjude.sjcrh.local>


Hello there,
After configure and running 'make' I get the following error (at the
end):

/usr/bin/ld: cannot find -lX11
Collect2: ld returned to exit status
make[2]: *** [aaindexextract] error 1
make[1]: *** [check-recursive] error 1

under /usr/bin/ld I do have X11 and my xterm works just fine.

After running 'make install' I notice similar errors as above.

Bottom line emboss does not run on my machine...

Help!


Suraj Mukatira




From anoop.rajendra at gmail.com  Thu Sep 14 13:24:22 2006
From: anoop.rajendra at gmail.com (Anoop Rajendra)
Date: Thu, 14 Sep 2006 10:24:22 -0700
Subject: [EMBOSS] installing EMBOSS-4.0.0 in ubuntu
In-Reply-To: <F2235647AC878D438F09255C39842FBC1563A319@SJMEMXMB03.stjude.sjcrh.local>
References: <F2235647AC878D438F09255C39842FBC1563A319@SJMEMXMB03.stjude.sjcrh.local>
Message-ID: <E768DD8D-CAD6-4B25-95AE-15728D25E488@gmail.com>

You need the X11 devel packages. On Ubuntu, I believe they are named  
xorg-x11-devel (or permutations thereof).

-anoop

On Sep 14, 2006, at 9:14 AM, Mukatira, Suraj wrote:

>
> Hello there,
> After configure and running 'make' I get the following error (at the
> end):
>
> /usr/bin/ld: cannot find -lX11
> Collect2: ld returned to exit status
> make[2]: *** [aaindexextract] error 1
> make[1]: *** [check-recursive] error 1
>
> under /usr/bin/ld I do have X11 and my xterm works just fine.
>
> After running 'make install' I notice similar errors as above.
>
> Bottom line emboss does not run on my machine...
>
> Help!
>
>
> Suraj Mukatira
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss



From charles-listes-emboss at plessy.org  Thu Sep 14 20:38:24 2006
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Fri, 15 Sep 2006 09:38:24 +0900
Subject: [EMBOSS] installing EMBOSS-4.0.0 in ubuntu
In-Reply-To: <E768DD8D-CAD6-4B25-95AE-15728D25E488@gmail.com>
References: <F2235647AC878D438F09255C39842FBC1563A319@SJMEMXMB03.stjude.sjcrh.local>
	<E768DD8D-CAD6-4B25-95AE-15728D25E488@gmail.com>
Message-ID: <20060915003824.GB10859@kunpuu.plessy.org>

Le Thu, Sep 14, 2006 at 10:24:22AM -0700, Anoop Rajendra a ?crit :
> You need the X11 devel packages. On Ubuntu, I believe they are named  
> xorg-x11-devel (or permutations thereof).

Hi all,

On Debian systems, I think that the following packages have to be
installed in order to builid EMBOSS (the first two being related to X).
It should not be very different on an Ubuntu system, as it is based on
Debian.

libx11-dev, x-dev, libgdchart-gd2-xpm-dev, zlib1g-dev, libpng12-dev

Good luck,

-- 
Charles Plessy
Debian-Med packaging team
http://www.debian.org/devel/debian-med/


From imadnansyed at yahoo.com  Fri Sep 15 08:29:46 2006
From: imadnansyed at yahoo.com (Adnan Shahzad)
Date: Fri, 15 Sep 2006 05:29:46 -0700 (PDT)
Subject: [EMBOSS] EMBOSS running on server (problems)
In-Reply-To: <20060913080756.GA24935@bigben.ulb.ac.be>
Message-ID: <20060915122946.30996.qmail@web61221.mail.yahoo.com>

Hello Guy Bottu,
  well i am again ending up in more issue and now this time as you said 
  in my "httpd.conf" the command was 
  user Apache
  and 
  group Apache
  i have replace Apache with nobody which i used in catch.c file.
   
  but now its giving me this error 
   
  "Internal Server Error
  The server encountered an internal error or misconfiguration and was unable to complete your request.
  Please contact the server administrator, root at localhost and inform them of the time the error occurred, and anything you might have done that may have caused the error.
  More information about this error may be available in the server error log.
   
  one more thing if i run from Windows Browser what should be my login on the win DOMAIN.
   
  Help me out buddy
  Regards,
   
  
---------------------------------
       

Guy Bottu <gbottu at ben.vub.ac.be> wrote:
  
Take a look at the file catch.c in the installation directory. It 
contains a line :
#define NOBODY "XXX"
In httpd.conf or maybe some other file in the configuration of your WWW 
server there should be a line :
User XXX
Both should match. XXX is the name of the user that is running the WWW 
server. Usually it is "root" that starts up the httpd demon, but then the 
program shifts user to a user "www", "nobody" or whatever, who has 
limited rights, e.g. not the right to run a shell. The wEMBOSS master 
program catch checks whether it has been started by the user who is 
running the httpd server and then shifts to the user who typed in his 
username+password ; if catch has been started by another user, it exits 
with the error message you saw. All this is for evident security reasons.

The wEMBOSS installation script asks you which user is running the WWW 
server. Try to figure out who that user is and run the installation 
script again.

Guy




  Adnan Shahzad Research Officer Department of Bioinformatics National Centre of Excellence in Molecular Biology Lahore, Pakistan.
  web: www.cemb.edu.pk Off:- 042-5423952 Ext. 303 Cell:- 0300-5337765
   


 		
---------------------------------
Stay in the know. Pulse on the new Yahoo.com.  Check it out. 


From imadnansyed at yahoo.com  Sat Sep 16 00:23:47 2006
From: imadnansyed at yahoo.com (Adnan Shahzad)
Date: Fri, 15 Sep 2006 21:23:47 -0700 (PDT)
Subject: [EMBOSS] EMBOSS running on server (problems)
In-Reply-To: <20060915181224.GA25610@bigben.ulb.ac.be>
Message-ID: <20060916042347.52345.qmail@web61213.mail.yahoo.com>

Hello Guy and every one
  well yes i checked in the log file and it gives one very strange error which i am not able to understand and that is...in the log file it gives me this error 
   
  Premature end of script headers: catch, referer: http://linwin/wEMBOSS/wEMBOSS.html
  
any thoughts on this
   
  Regards
Guy Bottu <gbottu at ben.vub.ac.be> wrote:
  On Fri, Sep 15, 2006 at 05:29:46AM -0700, Adnan Shahzad wrote:
> but now its giving me this error 
> 
> "Internal Server Error
> The server encountered an internal error or misconfiguration and was unable to complete your request.
> Please contact the server administrator, root at localhost and inform them of the time the error occurred, and anything you might have done that may have caused the error.
> More information about this error may be available in the server error log.

Oops, it is becoming tricky now. One possible way to diagnose the problem 
is to, as the message suggests, look in the error_log file of Apache and 
see what lines related to wEMBOSS say.



  Adnan Shahzad Research Officer Department of Bioinformatics National Centre of Excellence in Molecular Biology Lahore, Pakistan.
  web: www.cemb.edu.pk Off:- 042-5423952 Ext. 303 Cell:- 0300-5337765
   


 			
---------------------------------
Get your own web address for just $1.99/1st yr. We'll help. Yahoo! Small Business.


From imadnansyed at yahoo.com  Sat Sep 16 05:29:33 2006
From: imadnansyed at yahoo.com (Adnan Shahzad)
Date: Sat, 16 Sep 2006 02:29:33 -0700 (PDT)
Subject: [EMBOSS] Jemboss help
Message-ID: <20060916092933.23943.qmail@web61225.mail.yahoo.com>

Hello every body,
   
  can any one  please tell me that in the Jemboss when you install it. it says to install Jemboss run the "installer script" i am unable to find that script can you tell me how to get hold of that.
  Regards,


  Adnan Shahzad Research Officer Department of Bioinformatics National Centre of Excellence in Molecular Biology Lahore, Pakistan.
  web: www.cemb.edu.pk Off:- 042-5423952 Ext. 303 Cell:- 0300-5337765
   


 		
---------------------------------
Get your email and more, right on the  new Yahoo.com 


From imadnansyed at yahoo.com  Mon Sep 18 08:30:55 2006
From: imadnansyed at yahoo.com (Adnan Shahzad)
Date: Mon, 18 Sep 2006 05:30:55 -0700 (PDT)
Subject: [EMBOSS] EMBOSS EXPLORER help
Message-ID: <20060918123055.78267.qmail@web61221.mail.yahoo.com>

Hello every one 
  I have installed EMBOSS EXPLORER but the issue is that how to run it in the in the explorer. Their is nothing written in Read me file so any wise thoughts on that.
  Regards
   
   
   
     



  Adnan Shahzad Research Officer Department of Bioinformatics National Centre of Excellence in Molecular Biology Lahore, Pakistan.
  web: www.cemb.edu.pk Off:- 042-5423952 Ext. 303 Cell:- 0300-5337765
   


 		
---------------------------------
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From abhishek.vit at gmail.com  Mon Sep 18 12:22:31 2006
From: abhishek.vit at gmail.com (Abhishek Pratap)
Date: Mon, 18 Sep 2006 21:52:31 +0530
Subject: [EMBOSS] Problem Installing Jemboss
Message-ID: <be9b52410609180922j602e1f40le2aa0444ff20fa5@mail.gmail.com>

I am unable to install jemboss on solaris 10. with all the dependencies
installed (png, gd etc) i am getting this error.


This is the error i get each

------------------------- WARNING ----------------------------

The script has detected that /usr/include/gd.h
does not exist

Download gd from
       http://www.boutell.com/gd/

For details see the EMBOSS admin guide:
http://emboss.sourceforge.net/admin/

To exit use Control C or press return to continue.

--------------------------------------------------------------



>>>>>
the gd.h file is allready present in the /usr/include

Can someone guide me  on this

-- 
-----------------------------
Abhishek Pratap
Third Year
Bioinformatics
School of Biotechnology & Chemical Eng
VIT
Vellore.
INDIA
Ph:   (91)-416-3206020
Mob: (91)-9843181010


From andrespinzon at gmail.com  Mon Sep 18 13:22:24 2006
From: andrespinzon at gmail.com (Andres Pinzon)
Date: Mon, 18 Sep 2006 12:22:24 -0500
Subject: [EMBOSS] Fwd:  EMBOSS EXPLORER help
In-Reply-To: <8968fc7e0609181022l64359803l3084ba64a8474cba@mail.gmail.com>
References: <20060918123055.78267.qmail@web61221.mail.yahoo.com>
	<8968fc7e0609181022l64359803l3084ba64a8474cba@mail.gmail.com>
Message-ID: <8968fc7e0609181022l5e83c918h87bc87d02ebc292c@mail.gmail.com>

---------- Forwarded message ----------
From: Andres Pinzon <andrespinzon at gmail.com>
Date: Sep 18, 2006 12:22 PM
Subject: Re: [EMBOSS] EMBOSS EXPLORER help
To: Adnan Shahzad <imadnansyed at yahoo.com>


On 9/18/06, Adnan Shahzad <imadnansyed at yahoo.com> wrote:
> Hello every one
>   I have installed EMBOSS EXPLORER but the issue is that how to run it in the in the explorer. Their is nothing written in Read me file so any wise thoughts on that.

hmmm... your problem is not is not complete clear for me but...
Where did you installed it? It should be somewhere in your webserver
document root, so you can acces iit typing the following:
http://localhost/INSTALL_DIR/

just change INSTALL_DIR for the actual name of the emboss explorer
installation dir. If it was installed in an user space the following
could help:
http://localhost/~USERNAME/

Of course, change user name for the user who did the installation.

--
Andr?s Pinz?n cPh.D.
[http://www.andrespinzon.com]
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768


-- 
Andr?s Pinz?n cPh.D.
[http://www.andrespinzon.com]
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768



From Suraj.Mukatira at STJUDE.ORG  Mon Sep 18 15:54:21 2006
From: Suraj.Mukatira at STJUDE.ORG (Mukatira, Suraj)
Date: Mon, 18 Sep 2006 14:54:21 -0500
Subject: [EMBOSS] EMBOSS EXPLORER installation help
Message-ID: <F2235647AC878D438F09255C39842FBC157626B5@SJMEMXMB03.stjude.sjcrh.local>

Hi all,
I have questions regarding emboss explorer installation. Attached is the
explorer configuration file

I have emboss4.0 running in my linux machine: /usr/local/bin and
/var/www/emboss

After following instructions on the emboss explorer installation I
cannot see the webpage:
Not Found
The requested URL /cgi-bin/emboss/intro was not found on this server.

Not Found
The requested URL /cgi-bin/emboss/menu was not found on this server

Here are some directory structures:

drwxrwxr-x  2 mukatira mukatira   4096 2006-09-15 14:02 cgi-bin
drwxr-xr-x  6 mukatira mukatira   4096 2006-09-18 13:58 emboss
drwxrwxr-x  3 mukatira mukatira   4096 2006-09-15 14:02 html
-rw-r--r--  1 mukatira mukatira   1457 2006-09-11 14:28 index.html
$>:/var/www$ pwd
/var/www

Under cgi-bin I do not see a folder 'emboss'

$>/var/www/cgi-bin$ ls -l
-rwxrwxr-x 1 root root 110 2006-09-18 14:34 emboss
$>:/var/www/cgi-bin$ more emboss
#!/usr/bin/perl

use strict;
use warnings;

use EMBOSS::GUI;

my $emboss = EMBOSS::GUI->new();
$emboss->go();




Thanks in anticipation.
Also, what is the best way to completely uninstall emboss. 
-------------- next part --------------
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From golharam at umdnj.edu  Mon Sep 18 17:42:03 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Mon, 18 Sep 2006 17:42:03 -0400
Subject: [EMBOSS] EMBOSS EXPLORER installation help
In-Reply-To: <F2235647AC878D438F09255C39842FBC157626B5@SJMEMXMB03.stjude.sjcrh.local>
Message-ID: <016a01c6db6b$4abd4760$2f01a8c0@GOLHARMOBILE1>

Where there any errors from the install script you ran?  

Are you able to see your main page?  http://<servername>/cgi-bin/emboss?



> -----Original Message-----
> From: emboss-bounces at lists.open-bio.org 
> [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of 
> Mukatira, Suraj
> Sent: Monday, September 18, 2006 3:54 PM
> To: emboss at emboss.open-bio.org
> Subject: [EMBOSS] EMBOSS EXPLORER installation help
> 
> 
> Hi all,
> I have questions regarding emboss explorer installation. 
> Attached is the explorer configuration file
> 
> I have emboss4.0 running in my linux machine: /usr/local/bin 
> and /var/www/emboss
> 
> After following instructions on the emboss explorer 
> installation I cannot see the webpage: Not Found The 
> requested URL /cgi-bin/emboss/intro was not found on this server.
> 
> Not Found
> The requested URL /cgi-bin/emboss/menu was not found on this server
> 
> Here are some directory structures:
> 
> drwxrwxr-x  2 mukatira mukatira   4096 2006-09-15 14:02 cgi-bin
> drwxr-xr-x  6 mukatira mukatira   4096 2006-09-18 13:58 emboss
> drwxrwxr-x  3 mukatira mukatira   4096 2006-09-15 14:02 html
> -rw-r--r--  1 mukatira mukatira   1457 2006-09-11 14:28 index.html
> $>:/var/www$ pwd
> /var/www
> 
> Under cgi-bin I do not see a folder 'emboss'
> 
> $>/var/www/cgi-bin$ ls -l
> -rwxrwxr-x 1 root root 110 2006-09-18 14:34 emboss 
> $>:/var/www/cgi-bin$ more emboss #!/usr/bin/perl
> 
> use strict;
> use warnings;
> 
> use EMBOSS::GUI;
> 
> my $emboss = EMBOSS::GUI->new();
> $emboss->go();
> 
> 
> 
> 
> Thanks in anticipation.
> Also, what is the best way to completely uninstall emboss. 
> 



From Suraj.Mukatira at STJUDE.ORG  Mon Sep 18 17:42:57 2006
From: Suraj.Mukatira at STJUDE.ORG (Mukatira, Suraj)
Date: Mon, 18 Sep 2006 16:42:57 -0500
Subject: [EMBOSS] EMBOSS EXPLORER installation help.    .
Message-ID: <F2235647AC878D438F09255C39842FBC157627EB@SJMEMXMB03.stjude.sjcrh.local>


No.

http://10.1.6.145/cgi-bin/emboss/

Not Found
The requested URL /cgi-bin/emboss/ was not found on this server.

-----Original Message-----
From: Ryan Golhar [mailto:golharam at umdnj.edu] 
Sent: Monday, September 18, 2006 4:42 PM
To: Mukatira, Suraj
Cc: emboss at emboss.open-bio.org
Subject: RE: [EMBOSS] EMBOSS EXPLORER installation help. .

Where there any errors from the install script you ran?  

Are you able to see your main page?  http://<servername>/cgi-bin/emboss?



> -----Original Message-----
> From: emboss-bounces at lists.open-bio.org 
> [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of 
> Mukatira, Suraj
> Sent: Monday, September 18, 2006 3:54 PM
> To: emboss at emboss.open-bio.org
> Subject: [EMBOSS] EMBOSS EXPLORER installation help
> 
> 
> Hi all,
> I have questions regarding emboss explorer installation. 
> Attached is the explorer configuration file
> 
> I have emboss4.0 running in my linux machine: /usr/local/bin 
> and /var/www/emboss
> 
> After following instructions on the emboss explorer 
> installation I cannot see the webpage: Not Found The 
> requested URL /cgi-bin/emboss/intro was not found on this server.
> 
> Not Found
> The requested URL /cgi-bin/emboss/menu was not found on this server
> 
> Here are some directory structures:
> 
> drwxrwxr-x  2 mukatira mukatira   4096 2006-09-15 14:02 cgi-bin
> drwxr-xr-x  6 mukatira mukatira   4096 2006-09-18 13:58 emboss
> drwxrwxr-x  3 mukatira mukatira   4096 2006-09-15 14:02 html
> -rw-r--r--  1 mukatira mukatira   1457 2006-09-11 14:28 index.html
> $>:/var/www$ pwd
> /var/www
> 
> Under cgi-bin I do not see a folder 'emboss'
> 
> $>/var/www/cgi-bin$ ls -l
> -rwxrwxr-x 1 root root 110 2006-09-18 14:34 emboss 
> $>:/var/www/cgi-bin$ more emboss #!/usr/bin/perl
> 
> use strict;
> use warnings;
> 
> use EMBOSS::GUI;
> 
> my $emboss = EMBOSS::GUI->new();
> $emboss->go();
> 
> 
> 
> 
> Thanks in anticipation.
> Also, what is the best way to completely uninstall emboss. 
> 






From golharam at umdnj.edu  Mon Sep 18 17:58:40 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Mon, 18 Sep 2006 17:58:40 -0400
Subject: [EMBOSS] EMBOSS EXPLORER installation help.    .
In-Reply-To: <F2235647AC878D438F09255C39842FBC157627EB@SJMEMXMB03.stjude.sjcrh.local>
Message-ID: <016e01c6db6d$9d61d330$2f01a8c0@GOLHARMOBILE1>

Sounds like something is wrong with your cgi handler.  Are you able to
execute any cgi scripts in cgi-bin?  If not, can you include a copy of
your httpd.conf file and the error from /var/log/httpd/error_log?


> -----Original Message-----
> From: Mukatira, Suraj [mailto:Suraj.Mukatira at stjude.org] 
> Sent: Monday, September 18, 2006 5:43 PM
> To: golharam at umdnj.edu
> Cc: emboss at emboss.open-bio.org
> Subject: RE: [EMBOSS] EMBOSS EXPLORER installation help. .
> 
> 
> 
> No.
> 
> http://10.1.6.145/cgi-bin/emboss/
> 
> Not Found
> The requested URL /cgi-bin/emboss/ was not found on this server.
> 
> -----Original Message-----
> From: Ryan Golhar [mailto:golharam at umdnj.edu] 
> Sent: Monday, September 18, 2006 4:42 PM
> To: Mukatira, Suraj
> Cc: emboss at emboss.open-bio.org
> Subject: RE: [EMBOSS] EMBOSS EXPLORER installation help. .
> 
> Where there any errors from the install script you ran?  
> 
> Are you able to see your main page?  
> http://<servername>/cgi-bin/emboss?
> 
> 
> 
> > -----Original Message-----
> > From: emboss-bounces at lists.open-bio.org
> > [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of 
> > Mukatira, Suraj
> > Sent: Monday, September 18, 2006 3:54 PM
> > To: emboss at emboss.open-bio.org
> > Subject: [EMBOSS] EMBOSS EXPLORER installation help
> > 
> > 
> > Hi all,
> > I have questions regarding emboss explorer installation.
> > Attached is the explorer configuration file
> > 
> > I have emboss4.0 running in my linux machine: /usr/local/bin
> > and /var/www/emboss
> > 
> > After following instructions on the emboss explorer
> > installation I cannot see the webpage: Not Found The 
> > requested URL /cgi-bin/emboss/intro was not found on this server.
> > 
> > Not Found
> > The requested URL /cgi-bin/emboss/menu was not found on this server
> > 
> > Here are some directory structures:
> > 
> > drwxrwxr-x  2 mukatira mukatira   4096 2006-09-15 14:02 cgi-bin
> > drwxr-xr-x  6 mukatira mukatira   4096 2006-09-18 13:58 emboss
> > drwxrwxr-x  3 mukatira mukatira   4096 2006-09-15 14:02 html
> > -rw-r--r--  1 mukatira mukatira   1457 2006-09-11 14:28 index.html
> > $>:/var/www$ pwd
> > /var/www
> > 
> > Under cgi-bin I do not see a folder 'emboss'
> > 
> > $>/var/www/cgi-bin$ ls -l
> > -rwxrwxr-x 1 root root 110 2006-09-18 14:34 emboss
> > $>:/var/www/cgi-bin$ more emboss #!/usr/bin/perl
> > 
> > use strict;
> > use warnings;
> > 
> > use EMBOSS::GUI;
> > 
> > my $emboss = EMBOSS::GUI->new();
> > $emboss->go();
> > 
> > 
> > 
> > 
> > Thanks in anticipation.
> > Also, what is the best way to completely uninstall emboss.
> > 
> 
> 



From pmr at ebi.ac.uk  Tue Sep 19 08:39:09 2006
From: pmr at ebi.ac.uk (pmr at ebi.ac.uk)
Date: Tue, 19 Sep 2006 13:39:09 +0100 (BST)
Subject: [EMBOSS] [Fwd: RE:  EMBOSS-Explorer Follow-up]
Message-ID: <1622.193.175.249.183.1158669549.squirrel@webmail.ebi.ac.uk>

Hi Ryan,

>> Aha ... tfm works, but tfm -html may fail.
>>
>> If the program fails to find the html file, it will check the
>> original
>> distribution directory. Unfortunately, if it does find an
>> html file ...
>> it may be from version 3. I forgot about the tfm -html option when we
moved the files.
>>
>> A fix will take a few days to test. EMBASSY html documentation is not
under the embassy package, so TFM will have to check the ACD file to
find the EMBASSY package name. Easy enough - several other
>> programs do
>> it - but needs quite a few tests to make sure it does it correctly in
all cases.

I have posted a fix (Fix 18, emboss/tfm.c and nucleus/emboss.[ch]) on the
FTP server ftp://emboss.open-bio.org/pub/EMBOSS/fixes

More information in the README.fixes file.

Apologies for this bug ... I completely forgot there was a -html option in
tfm ... but at least we now have a use for it :-)

regards.

Peter





From mthon at tamu.edu  Tue Sep 19 10:27:44 2006
From: mthon at tamu.edu (Michael Thon)
Date: Tue, 19 Sep 2006 09:27:44 -0500
Subject: [EMBOSS] showfeat: joining compound features
Message-ID: <D9F13423-1AF1-4863-A6FD-EFA254B7F913@tamu.edu>

Hello everyone - I am using showfeat to display blast similarity  
features that are stored in a gff file.  From the documentation, it  
looks like showfeat can display multiple exon features on the same  
line but can it also do this with similarity features?  Here is an  
example from my gff file:

Chr5:4535154,4542653    BLAST   similarity      2475     
5120    .       .       .       Target "ref|XP_468448.1|"
Chr5:4535154,4542653    BLAST   similarity      3142    3480     
388     +       .       Target "ref|XP_468448.1|" 141 225
Chr5:4535154,4542653    BLAST   similarity      4944    5120     
304     +       .       Target "ref|XP_468448.1|" 248 306
Chr5:4535154,4542653    BLAST   similarity      2475    2603     
216     +       .       Target "ref|XP_468448.1|" 66 108
Chr5:4535154,4542653    BLAST   similarity      2916    3017     
182     +       .       Target "ref|XP_468448.1|" 107 140

Also, is there an emboss program that does showfeat's functions but  
with a graphical, publication quality output?  I am thinking of a  
graphic with colored feature tracks, etc.
Thanks
Mike




From thomas.girke at ucr.edu  Tue Sep 19 11:08:44 2006
From: thomas.girke at ucr.edu (Thomas Girke)
Date: Tue, 19 Sep 2006 08:08:44 -0700
Subject: [EMBOSS] showfeat: joining compound features
In-Reply-To: <D9F13423-1AF1-4863-A6FD-EFA254B7F913@tamu.edu>
References: <D9F13423-1AF1-4863-A6FD-EFA254B7F913@tamu.edu>
Message-ID: <20060919150844.GA21474@bioinfo.ucr.edu>

Micheal,

If you know R a little bit then you may want to try this R script. 
http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/featureMap.txt

I often use this script for plotting position information of all kinds of EMBOSS
programs onto genes and chromosomes.

To demo the utility of the script, simply paste this command into the R console:
source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/featureMap.txt")

Best,
Thomas

On Tue 09/19/06 09:27, Michael Thon wrote:
> Hello everyone - I am using showfeat to display blast similarity  
> features that are stored in a gff file.  From the documentation, it  
> looks like showfeat can display multiple exon features on the same  
> line but can it also do this with similarity features?  Here is an  
> example from my gff file:
> 
> Chr5:4535154,4542653    BLAST   similarity      2475     
> 5120    .       .       .       Target "ref|XP_468448.1|"
> Chr5:4535154,4542653    BLAST   similarity      3142    3480     
> 388     +       .       Target "ref|XP_468448.1|" 141 225
> Chr5:4535154,4542653    BLAST   similarity      4944    5120     
> 304     +       .       Target "ref|XP_468448.1|" 248 306
> Chr5:4535154,4542653    BLAST   similarity      2475    2603     
> 216     +       .       Target "ref|XP_468448.1|" 66 108
> Chr5:4535154,4542653    BLAST   similarity      2916    3017     
> 182     +       .       Target "ref|XP_468448.1|" 107 140
> 
> Also, is there an emboss program that does showfeat's functions but  
> with a graphical, publication quality output?  I am thinking of a  
> graphic with colored feature tracks, etc.
> Thanks
> Mike
> 
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
> 

-- 
Thomas Girke, Ph.D.
1008 Noel T. Keen Hall
Center for Plant Cell Biology (CEPCEB)
University of California
Riverside, CA 92521

E-mail: thomas.girke at ucr.edu
Website: http://faculty.ucr.edu/~tgirke
Ph: 951-827-2469
Fax: 951-827-4437


From mthon at tamu.edu  Thu Sep 21 10:04:02 2006
From: mthon at tamu.edu (Michael Thon)
Date: Thu, 21 Sep 2006 09:04:02 -0500
Subject: [EMBOSS] showfeat: joining compound features
In-Reply-To: <20060919150844.GA21474@bioinfo.ucr.edu>
References: <D9F13423-1AF1-4863-A6FD-EFA254B7F913@tamu.edu>
	<20060919150844.GA21474@bioinfo.ucr.edu>
Message-ID: <C4446B21-D1BA-487E-BF96-CC58EC685409@tamu.edu>

Hi Thomas - Thanks for the script, I'm going to try it out.  My need  
the other day was for an easy way to display features that I could  
show to my class.  Showfeat ended up working alright so that's what  
we're using at the moment.  gff2ps is also good at making graphics  
but I thought there should be an emboss way to do it too.
cheers
Mike

On Sep 19, 2006, at 10:08 AM, Thomas Girke wrote:

> Micheal,
>
> If you know R a little bit then you may want to try this R script.
> http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/ 
> featureMap.txt
>
> I often use this script for plotting position information of all  
> kinds of EMBOSS
> programs onto genes and chromosomes.
>
> To demo the utility of the script, simply paste this command into  
> the R console:
> source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/ 
> My_R_Scripts/featureMap.txt")
>
> Best,
> Thomas
>
> On Tue 09/19/06 09:27, Michael Thon wrote:
>> Hello everyone - I am using showfeat to display blast similarity
>> features that are stored in a gff file.  From the documentation, it
>> looks like showfeat can display multiple exon features on the same
>> line but can it also do this with similarity features?  Here is an
>> example from my gff file:
>>
>> Chr5:4535154,4542653    BLAST   similarity      2475
>> 5120    .       .       .       Target "ref|XP_468448.1|"
>> Chr5:4535154,4542653    BLAST   similarity      3142    3480
>> 388     +       .       Target "ref|XP_468448.1|" 141 225
>> Chr5:4535154,4542653    BLAST   similarity      4944    5120
>> 304     +       .       Target "ref|XP_468448.1|" 248 306
>> Chr5:4535154,4542653    BLAST   similarity      2475    2603
>> 216     +       .       Target "ref|XP_468448.1|" 66 108
>> Chr5:4535154,4542653    BLAST   similarity      2916    3017
>> 182     +       .       Target "ref|XP_468448.1|" 107 140
>>
>> Also, is there an emboss program that does showfeat's functions but
>> with a graphical, publication quality output?  I am thinking of a
>> graphic with colored feature tracks, etc.
>> Thanks
>> Mike
>>
>>
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>
> -- 
> Thomas Girke, Ph.D.
> 1008 Noel T. Keen Hall
> Center for Plant Cell Biology (CEPCEB)
> University of California
> Riverside, CA 92521
>
> E-mail: thomas.girke at ucr.edu
> Website: http://faculty.ucr.edu/~tgirke
> Ph: 951-827-2469
> Fax: 951-827-4437



From David.Bauer at SCHERING.DE  Thu Sep 21 03:39:47 2006
From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE)
Date: Thu, 21 Sep 2006 09:39:47 +0200
Subject: [EMBOSS] showfeat: joining compound features
In-Reply-To: <20060919150844.GA21474@bioinfo.ucr.edu>
Message-ID: <OF3D51E382.B49D26C3-ONC12571F0.0029A814-C12571F0.002A1834@schering.de>


Hi,

if your data are in gff format you could also try gff2ps:
http://www1.imim.es/software/gfftools/GFF2PS.html
Within EMBOSS there is also an application lindna but it has its own input
format so you must first convert your gff file to lindna input.

HTH,
David.

emboss-bounces at lists.open-bio.org schrieb am 19/09/2006 17:08:44:

> Micheal,
>
> If you know R a little bit then you may want to try this R script.
>
http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/featureMap.txt

>
> I often use this script for plotting position information of all
> kinds of EMBOSS
> programs onto genes and chromosomes.
>
> To demo the utility of the script, simply paste this command into
> the R console:
> source("http://faculty.ucr.
> edu/~tgirke/Documents/R_BioCond/My_R_Scripts/featureMap.txt")
>
> Best,
> Thomas
>
> On Tue 09/19/06 09:27, Michael Thon wrote:
> > Hello everyone - I am using showfeat to display blast similarity
> > features that are stored in a gff file.  From the documentation, it
> > looks like showfeat can display multiple exon features on the same
> > line but can it also do this with similarity features?  Here is an
> > example from my gff file:
> >
> > Chr5:4535154,4542653    BLAST   similarity      2475
> > 5120    .       .       .       Target "ref|XP_468448.1|"
> > Chr5:4535154,4542653    BLAST   similarity      3142    3480
> > 388     +       .       Target "ref|XP_468448.1|" 141 225
> > Chr5:4535154,4542653    BLAST   similarity      4944    5120
> > 304     +       .       Target "ref|XP_468448.1|" 248 306
> > Chr5:4535154,4542653    BLAST   similarity      2475    2603
> > 216     +       .       Target "ref|XP_468448.1|" 66 108
> > Chr5:4535154,4542653    BLAST   similarity      2916    3017
> > 182     +       .       Target "ref|XP_468448.1|" 107 140
> >
> > Also, is there an emboss program that does showfeat's functions but
> > with a graphical, publication quality output?  I am thinking of a
> > graphic with colored feature tracks, etc.
> > Thanks
> > Mike
> >
> >
> > _______________________________________________
> > EMBOSS mailing list
> > EMBOSS at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/emboss
> >
>
> --
> Thomas Girke, Ph.D.
> 1008 Noel T. Keen Hall
> Center for Plant Cell Biology (CEPCEB)
> University of California
> Riverside, CA 92521
>
> E-mail: thomas.girke at ucr.edu
> Website: http://faculty.ucr.edu/~tgirke
> Ph: 951-827-2469
> Fax: 951-827-4437
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss



From tjc at sanger.ac.uk  Mon Sep 25 09:07:53 2006
From: tjc at sanger.ac.uk (Tim Carver)
Date: Mon, 25 Sep 2006 14:07:53 +0100
Subject: [EMBOSS] Problem Installing Jemboss
In-Reply-To: <be9b52410609180922j602e1f40le2aa0444ff20fa5@mail.gmail.com>
Message-ID: <C13D9339.1CDA6%tjc@sanger.ac.uk>

Hi

For EMBOSS you need zlib, libgd and libpng all in one place and this is what
the script checks for. So you may need to ensure that is the case and if
necessary use the  --with-pngdriver (on option when you run the install
script) flag to define where.

Regards
Tim Carver


On 18/9/06 17:22, "Abhishek Pratap" <abhishek.vit at gmail.com> wrote:

> I am unable to install jemboss on solaris 10. with all the dependencies
> installed (png, gd etc) i am getting this error.
> 
> 
> This is the error i get each
> 
> ------------------------- WARNING ----------------------------
> 
> The script has detected that /usr/include/gd.h
> does not exist
> 
> Download gd from
>        http://www.boutell.com/gd/
> 
> For details see the EMBOSS admin guide:
> http://emboss.sourceforge.net/admin/
> 
> To exit use Control C or press return to continue.
> 
> --------------------------------------------------------------
> 
> 
> 
>>>>>> 
> the gd.h file is allready present in the /usr/include
> 
> Can someone guide me  on this




From sea99.wang at gmail.com  Mon Sep 25 12:30:57 2006
From: sea99.wang at gmail.com (Sea)
Date: Tue, 26 Sep 2006 00:30:57 +0800
Subject: [EMBOSS] EMBOSS Explorer "bad substitution"
Message-ID: <4f3a50530609250930x3c68292h32eda9207fb5124f@mail.gmail.com>

Hello Everybody,

I met another problem....
When I ran "install" of emboss explorer
and it started to do the job,
but I always got this message "bad substitution" and then quit.
Could any expenience friends provide me a solution?
Thanks a lot!

Here is the logs:


# ./install
installing EMBOSS Explorer perl modules...

'PREREQ_FATAL' is not a known MakeMaker parameter name.
Writing Makefile for EMBOSS::GUI
Manifying blib/man3/EMBOSS::GUI.3
Manifying blib/man3/EMBOSS::GUI::XHTML.3
Manifying blib/man3/EMBOSS::GUI::Conf.3
Manifying blib/man3/EMBOSS::ACD.3
Manifying blib/man3/EMBOSS::GUI.3
Installing /usr/perl5/site_perl/5.6.1/EMBOSS/GUI.pm
Installing /usr/perl5/site_perl/5.6.1/EMBOSS/ACD.pm
Installing /usr/perl5/site_perl/5.6.1/EMBOSS/GUI/XHTML.pm
Installing /usr/perl5/site_perl/5.6.1/EMBOSS/GUI/Conf.pm
Installing /usr/perl5/5.6.1/man/man3/EMBOSS::GUI.3
Installing /usr/perl5/5.6.1/man/man3/EMBOSS::GUI::XHTML.3
Installing /usr/perl5/5.6.1/man/man3/EMBOSS::GUI::Conf.3
Installing /usr/perl5/5.6.1/man/man3/EMBOSS::ACD.3
Writing
/usr/perl5/site_perl/5.6.1/sun4-solaris-64int/auto/EMBOSS/GUI/.packlist
Appending installation info to
/usr/perl5/5.6.1/lib/sun4-solaris-64int/perllocal.pod
`install' is up to date.
installing EMBOSS Explorer GUI components...


I need to collect some information in order to install EMBOSS Explorer:
./install: embossversion: not found
-e Where was EMBOSS installed?
        (default is /usr/local)
/bioserver/emboss/share
-e Where should the EMBOSS Explorer HTML files be installed?
        (default is /var/www/html/emboss)
/bioserver/emboss/share/GUI/htdocs
-e What is the URL prefix corresponding to the HTML directory above?
        (default is /emboss)
 [use default setting]
-e Where should the EMBOSS Explorer CGI script be installed?
        (default is /var/www/cgi-bin/emboss)
/bioserver/emboss/share/GUI/cgi-bin
./install: bad substitution     [<-- always got this....  : ( ]


From tjc at sanger.ac.uk  Tue Sep 26 05:26:28 2006
From: tjc at sanger.ac.uk (Tim Carver)
Date: Tue, 26 Sep 2006 10:26:28 +0100
Subject: [EMBOSS] Jemboss problems with fuzzpro and fuzznuc
In-Reply-To: <4507DB32.7040903@cancer.org.uk>
Message-ID: <C13EB0D4.1D332%tjc@sanger.ac.uk>

Hi Neil

Thanks for your message. This is a known bug. As far as I understand the new
pattern qualifier has associated qualifiers -pmismatch (also pformat and
pname) which Jemboss does not know about (yet) as it just treats the pattern
as a string.

Cheers
Tim

On 13/9/06 11:19, "Neil Brookes" <neil.brookes at cancer.org.uk> wrote:

> Hi,
> 
> I think I have unearthed an issue with fuzzpro/fuzznuz and EMBOSS 4.0.0
> The old version in 3.0.0 had a '-mismatch' option. This has changed in
> version 4.0.0 to '-pmismatch'.
> 
> The 'mismatch' integer element seems to have been removed from the
> fuzzpro/nuc ACD files.
> I'm not sure how/when Jemboss parses the ACD flies, but it doesn't seem
> to be allowing for the  new '-pmismatch' option, and users are unable to
> specify a value.
> 
> any ideas ?
> 
> cheers
> Neil




From gbottu at ben.vub.ac.be  Thu Sep 28 09:57:40 2006
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Thu, 28 Sep 2006 15:57:40 +0200
Subject: [EMBOSS] case sensitive identifiers - Checked by AntiVir DEMO
	version -
Message-ID: <20060928135740.GA14320@bigben.ulb.ac.be>

	Dear colleagues,

Thure Etzold, the developer of SRS, once said "You cannot imagine anything 
that crazy or there is at least one database manager who really does it". 
While trying to put in our MRS server databanks with the protein and 
nucleic acid sequences extracted from the PDB, I bumped on the following 
problem : some have identifiers only different by case. E.g. there is a 
1fnt_A and a 1fnt_a. Now, most bioinformatic software is not case 
sensitive. I understand that MRS stores indices so that they can be 
displayed in their original case, but can only be searched
case-insensitively ; it does automatically modify redundant indices, e.g. 
1fnt_a is stored as 1fnt_a_12835. This is however not ideal. Should MRS 
be adapted so that it can handle case sensitive indices ? This will 
however not solve everything, since other software like EMBOSS or GCG is 
also case insensitive. My idea is to let the MRS parser store 1fnt_aLC
(LC means lowercase) as identifier. A user can then search for the 
sequence he needs in MRS and in EMBOSS (if the EMBOSS installation uses 
MRS as databank access mechanism) ask for the sequence pdbprot:1fnt_alc.
This would of course also work with 1fnt_a_12835 but it avoids the use of 
a meaningless and irreproducible number. Anybody a comment ?

	Regards,
	Guy Bottu,
	Belgian EMBnet Node



From pmr at ebi.ac.uk  Thu Sep 28 10:32:36 2006
From: pmr at ebi.ac.uk (Peter Rice)
Date: Thu, 28 Sep 2006 15:32:36 +0100
Subject: [EMBOSS] [Mrs-user] case sensitive identifiers
In-Reply-To: <20060928135740.GA14320@bigben.ulb.ac.be>
References: <20060928135740.GA14320@bigben.ulb.ac.be>
Message-ID: <451BDD04.9040806@ebi.ac.uk>

Guy Bottu wrote:
> My idea is to let the MRS parser store 1fnt_aLC
> (LC means lowercase) as identifier. A user can then search for the 
> sequence he needs in MRS and in EMBOSS (if the EMBOSS installation uses 
> MRS as databank access mechanism) ask for the sequence pdbprot:1fnt_alc.
> This would of course also work with 1fnt_a_12835 but it avoids the use of 
> a meaningless and irreproducible number. Anybody a comment ?

Not a general solution, but for PDB chains you could use an extra 
underscore for the lower case ones.

For EMBOSS .... well, we could play with the way databases work. Not all 
access methods allow case sensitive searching, but we could fetch all 
entries and try to reject those that do not match. This would need 
something in the EMBOSS id. We already allow modifiers after the id to 
set sequence ranges pdbprot:1fbt_a[1:20] or we could add a qualifier 
-scasesensitive for all sequence inputs.

Peter


From gbottu at ben.vub.ac.be  Fri Sep 29 04:15:08 2006
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Fri, 29 Sep 2006 10:15:08 +0200
Subject: [EMBOSS] case sensitive identifiers - Checked by AntiVir DEMO
	version -
In-Reply-To: <451BDD04.9040806@ebi.ac.uk>
References: <20060928135740.GA14320@bigben.ulb.ac.be>
	<451BDD04.9040806@ebi.ac.uk>
Message-ID: <20060929081508.GA25906@bigben.ulb.ac.be>

On Thu, Sep 28, 2006 at 03:32:36PM +0100, Peter Rice wrote:
> For EMBOSS .... well, we could play with the way databases work. Not all 
> access methods allow case sensitive searching, but we could fetch all 
> entries and try to reject those that do not match. This would need 
> something in the EMBOSS id. We already allow modifiers after the id to 
> set sequence ranges pdbprot:1fbt_a[1:20] or we could add a qualifier 
> -scasesensitive for all sequence inputs.

For the moment our emboss.default contains :

DB pdbprot [ type: P format: fasta comment: 'protein sequences from PDB'
     methodquery: app app: "/nfsben/srs/bin/linux73/getz -e '[pdbprot-id:%s]'"
             methodall: direct dir: /nfsben/srs/data/blast/dbfb/pdb file: pdb
]

and seqret pdbprot:1ml5_s yields :

>1ml5_S 30S RIBOSOMAL PROTEIN S16
MVKIRLARFGSKHNPHYPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLKVDVERAR
YWLSVGAQPTDTARRLLRQAGVFRQEAREGA
>1ml5_s 50S RIBOSOMAL PROTEIN L22
MEAKAIARYVRISPRKVRLVVDLIRGKSLEEARNILRYTNKRGAYFVAKVLESAAANAVN
NHDMLEDRLYVKAAYVDEGPALKRVLPRARGRADIIKKRTSHITVILGEKHGK

So, your idea of fetching all entries and then parsing them would work 
for SRS. I however think that instead of an associated parameter  
-scasesensitive it would be better to have in the emboss.default syntax 
for DB entries an optional parameter case:. You should be able to handle 
the situation where it is appropriate to pass an id to a case sensitive 
search method and the situation where it is appropriate to parse the 
output of a case-insensitive search method. This can best be decided for each 
databank at EMBOSS site configuartion time, rather than at sequence 
retrieval time. What do you think ?

	Regards,
	Guy Bottu



From pmr at ebi.ac.uk  Fri Sep 29 04:28:22 2006
From: pmr at ebi.ac.uk (pmr at ebi.ac.uk)
Date: Fri, 29 Sep 2006 09:28:22 +0100 (BST)
Subject: [EMBOSS] case sensitive identifiers - Checked by AntiVir DEMO
	version -
In-Reply-To: <20060929081508.GA25906@bigben.ulb.ac.be>
References: <20060928135740.GA14320@bigben.ulb.ac.be>
	<451BDD04.9040806@ebi.ac.uk>
	<20060929081508.GA25906@bigben.ulb.ac.be>
Message-ID: <2023.86.132.219.183.1159518502.squirrel@webmail.ebi.ac.uk>

Dear Guy,

> So, your idea of fetching all entries and then parsing them would work
> for SRS. I however think that instead of an associated parameter
> -scasesensitive it would be better to have in the emboss.default syntax
> for DB entries an optional parameter case:. You should be able to handle
> the situation where it is appropriate to pass an id to a case sensitive
> search method and the situation where it is appropriate to parse the
> output of a case-insensitive search method. This can best be decided for
> each
> databank at EMBOSS site configuartion time, rather than at sequence
> retrieval time. What do you think ?

You are right. Excellent idea. I will do it ASAP.

It will mean a new attribute stored for sequence database access.

For the PDB case, really only the end of the ID is case-sensitive. Do you
think the database should be case-sensitive for the whole ID, or does it
make sense to check for a pattern as the case-sensitive part?

EMBOSS will initially read only one sequence for a seqall ... it does not
read in all the sequences and look for duplicates so we have to decide in
the emboss.defaults DB definition how to check a single ID (no way to read
them all and check for duplicates).

regardrs,

Peter




From pmr at ebi.ac.uk  Fri Sep 29 06:27:51 2006
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 29 Sep 2006 11:27:51 +0100
Subject: [EMBOSS] case sensitive identifiers
In-Reply-To: <20060929081508.GA25906@bigben.ulb.ac.be>
References: <20060928135740.GA14320@bigben.ulb.ac.be>
	<451BDD04.9040806@ebi.ac.uk>
	<20060929081508.GA25906@bigben.ulb.ac.be>
Message-ID: <451CF527.8040506@ebi.ac.uk>

Guy Bottu wrote:
> For the moment our emboss.default contains :
> 
> DB pdbprot [ type: P format: fasta comment: 'protein sequences from PDB'
>      methodquery: app app: "/nfsben/srs/bin/linux73/getz -e '[pdbprot-id:%s]'"
>              methodall: direct dir: /nfsben/srs/data/blast/dbfb/pdb file: pdb
> ]

That raises a new problem .... the "app" method will work, but "srs" and 
"srswww" will not.

They search for a pdbprot-acc match and there is no acc field.

I will add a new database attribute hasaccession (default "Y") so 
searches know whether the acc field can be used. Unfortunately the 
fields attribute is defined as "everything except id and acc" so I 
cannot use it.

So, there will be 2 new (and for the first time boolean) attributes for 
databases. To use them, you will need:

caseidmatch: "Y"
hasaccession: "N"

These will also be the first to use the default values for database 
attributes! All other default values are empty strings :-)

regards,

Peter


From charles-listes-emboss at plessy.org  Mon Sep  4 04:28:50 2006
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Mon, 4 Sep 2006 13:28:50 +0900
Subject: [EMBOSS] Manpage generator
Message-ID: <20060904042850.GC14634@kunpuu.plessy.org>

Dear emboss developpers,

I am a member of the Debian-med project, and we intend to provide Debian
packages for EMBOSS soon. First of all, if some persons reading this
mail would be interestd to participae to this effort, we are very open
to collaboration, and we even have dedicated facilities for this:

http://alioth.debian.org/projects/pkg-emboss/

It is part from the Debian policy that any program in the /usr/bin and
sister directories should have a man page, and EMBOSS programs do not
provide them, so I decided that I will develop a manpage generator.

For the moment, I intend to parse the .acd files, fill templates in the
DocBook format, and convert them using an xsl stylesheet. I welcome any
suggestion on how to parse the .acd files for this purpose (I have no
other plan than using brute force with perl).

Have a nice day,

-- 
Charles Plessy
http://charles.plessy.org
Wako, Saitama, Japan


From David.Bauer at schering.de  Mon Sep  4 05:54:01 2006
From: David.Bauer at schering.de (David.Bauer at schering.de)
Date: Mon, 4 Sep 2006 07:54:01 +0200
Subject: [EMBOSS] Antwort:  How to modify a program?
In-Reply-To: <001a01c654d4$6bfc13c0$1b02a8c0@tao>
Message-ID: <OFD521873A.74CBFA77-ONC12571DF.001FD412-C12571DF.00206DC4@schering.de>


Anything in ajax and nucleus is incorporated in the libraries libajax and
libnucleus.
So you must rebuild/reinstall  theses libraries.
Just run a 'make install' in the top emboss source dir and this will
rebuild the modified library and your application.
The make utility looks at the modification time of the files so it will
recompile only those which have been changed.

HTH,
David.

emboss-bounces at lists.open-bio.org schrieb am 31/03/2006 17:04:32:

> Hi,
>
>      I am new to Unix system, so sorry if it is a too simple question.
> I need to modify the DIGEST  program (\EMBOSS-4.0.0\emboss\digest)
> to change some rules for trypsin digestion. The part of the program that
> I need to modify is in another program (EMBOSS-4.0.0\nucleus\embprop.c).
> After modify the embprop program I compiled with gcc and got a embprop.o
> file. But when I ran the DIGEST program it still give the same results
and
> didn't
> change. Are there some steps that I missed?
>
>      Thanks a lot for your help!
>
>      Regards,
>
>      Tao
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss



From David.Bauer at schering.de  Mon Sep  4 06:57:54 2006
From: David.Bauer at schering.de (David.Bauer at schering.de)
Date: Mon, 4 Sep 2006 08:57:54 +0200
Subject: [EMBOSS] Antwort:  Manpage generator
In-Reply-To: <20060904042850.GC14634@kunpuu.plessy.org>
Message-ID: <OFEA4A36A9.0EB51F74-ONC12571DF.00259DD5-C12571DF.00264720@schering.de>


Hi,

there are a kind of manpages in text and html format provided with emboss.
They are installed in
<prefix>/share/EMBOSS/doc/html/emboss/apps
and
<prefix>/share/EMBOSS/doc/programs/text

The txt files are used by the emboss application 'tfm' which displays this
documentation like man does.
The html files are for developers of web interfaces.

If you want to parse ACD files you should have a look at the "emboss
explorer" web gui.
This uses perl modules to parse acd files and create the web interface
dynamically.

HTH,
David.


emboss-bounces at lists.open-bio.org schrieb am 04/09/2006 06:28:50:

> Dear emboss developpers,
>
> I am a member of the Debian-med project, and we intend to provide Debian
> packages for EMBOSS soon. First of all, if some persons reading this
> mail would be interestd to participae to this effort, we are very open
> to collaboration, and we even have dedicated facilities for this:
>
> http://alioth.debian.org/projects/pkg-emboss/
>
> It is part from the Debian policy that any program in the /usr/bin and
> sister directories should have a man page, and EMBOSS programs do not
> provide them, so I decided that I will develop a manpage generator.
>
> For the moment, I intend to parse the .acd files, fill templates in the
> DocBook format, and convert them using an xsl stylesheet. I welcome any
> suggestion on how to parse the .acd files for this purpose (I have no
> other plan than using brute force with perl).
>
> Have a nice day,
>
> --
> Charles Plessy
> http://charles.plessy.org
> Wako, Saitama, Japan
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss



From jison at ebi.ac.uk  Mon Sep  4 13:13:38 2006
From: jison at ebi.ac.uk (Jon Ison)
Date: Mon, 4 Sep 2006 14:13:38 +0100 (BST)
Subject: [EMBOSS] Question about make use of multiple fields indexing by
 dbxfasta or dbxflat
In-Reply-To: <000501c6c6f4$66aad770$be4de780@CIT.NIH.GOV>
References: <000501c6c6f4$66aad770$be4de780@CIT.NIH.GOV>
Message-ID: <34864.172.31.70.94.1157375618.squirrel@webmail.ebi.ac.uk>

Hi Jean

The short answer is, by adding extra fields, all programs that
read sequence(s) would benefit from increased flexibility in
how sequences may be specified on the command-line.

You can read about how to specify sequences using the Uniform
Sequence Address (USA) model here:
http://emboss.sourceforge.net/docs/themes/UniformSequenceAddress.html

(look under "The Full USA syntax")

If any applications absolutely required certain indexing then that
would be mentioned in the application documentation, accessible via:
http://emboss.sourceforge.net/apps/

Cheers

Jon



> Hello,
>
> I need to index swissprot data file from uniprot.org. They have two formats : fasta and flat available. I understand I
> can specify fields to be indexed. And there are more fields can be specified if using flat file with dbxflat. However,
> I am not sure how many programs in EMBOSS package will be benefit from specifying extra fields other than acc and id
> except 'seqret'? Could someone let me know how to find the answer? Thanks you very much in advance.
>
> Jean
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>




From aidanfindlater at gmail.com  Mon Sep  4 14:03:30 2006
From: aidanfindlater at gmail.com (Aidan Findlater)
Date: Mon, 4 Sep 2006 10:03:30 -0400
Subject: [EMBOSS] EMBOSS cai
Message-ID: <bd79799b0609040703x1d525d76oade13ca7763b4fd7@mail.gmail.com>

I'm trying to figure out what the appropriate table for calculating
the CAIs of fission yeast sequences.

The documentation says, "The default codon usage table 'Eyeastcai.cut'
was prepared from a set of S. pombe genes by Peter Rice." If you copy
the example in the documentation (that uses a fission yeast gene with
the Eyeastcai.cut table), you get the same results that they show.

However, if you look at the index of tables in EMBOSS's data
directory, it says that Eyeast_cai.cut is the
"Saccharomyces_cerevisiae original CAI set (Eyeastcai.cut)". The table
that is identified as being fission yeast gives very different
numbers.

Any clarification would be greatly appreciated!

Thanks,

Aidan Findlater


From pmr at ebi.ac.uk  Mon Sep  4 14:46:39 2006
From: pmr at ebi.ac.uk (pmr at ebi.ac.uk)
Date: Mon, 4 Sep 2006 15:46:39 +0100 (BST)
Subject: [EMBOSS] EMBOSS cai
In-Reply-To: <bd79799b0609040703x1d525d76oade13ca7763b4fd7@mail.gmail.com>
References: <bd79799b0609040703x1d525d76oade13ca7763b4fd7@mail.gmail.com>
Message-ID: <2099.82.68.212.94.1157381199.squirrel@webmail.ebi.ac.uk>

Dear Aidan,

> I'm trying to figure out what the appropriate table for calculating
> the CAIs of fission yeast sequences.
>
> The documentation says, "The default codon usage table 'Eyeastcai.cut'
> was prepared from a set of S. pombe genes by Peter Rice." If you copy
> the example in the documentation (that uses a fission yeast gene with
> the Eyeastcai.cut table), you get the same results that they show.

Oops. Confusion (missing line) in the documentation for the cai
application. We have tables for Saccharomyces cerevisiae and
Schizosaccharomyces pombe. Fission yeast is in Eschpo_cai.cut, cerevisiae
is in Eyeast_cai.cut. I will fix the docuemntation.

In previous releases of EMBOSS the names were Epombecai.cut and
Eyeastcai.cut. Release 4.0.0 has both names - future versions will use the
new names to make the species clearer.

I prepared both tables. Eyeast_cai.cut gives the published cerevisiae CAI
values (the tables do not quite match the current gene sequences).
Eschpo_cai.cut uses the same genes from S. pombe and is the one to use for
fission yeast. The tabel was set uip for the pombe sequencers at Sanger.
They may be able to give you more information about how useful the results
are.

Hope that helps,

Peter



From golharam at umdnj.edu  Tue Sep  5 16:39:22 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Tue, 05 Sep 2006 12:39:22 -0400
Subject: [EMBOSS] EMBOSS-Explorer & EMBOSS-4.0.0
Message-ID: <03f201c6d109$d725d710$2f01a8c0@GOLHARMOBILE1>

I recently installed EMBOSS 4 and am encountering the "unknown datatype
pattern"  error for fuzznuc (new to EMBOSS 4).  

Here's the URL:
http://serine.umdnj.edu/cgi-bin/emboss/fuzznuc  

I've been trying to get a hold of Luke but email is bouncing back...

Ryan



From maoj at helix.nih.gov  Tue Sep  5 18:35:25 2006
From: maoj at helix.nih.gov (Jean Mao)
Date: Tue, 5 Sep 2006 14:35:25 -0400
Subject: [EMBOSS] Question regarding seqret
Message-ID: <000001c6d11a$0db13530$be4de780@CIT.NIH.GOV>

Hi, 
I have a question hopefully someone can help me about it.

I downloaded the gbrvt1.seq file from ftp://ftp.ncbi.nih.gov/genbank/ as a test, gunzip and index it with dbxflat (I know it's not > than 2gb):

%  dbxflat -dbname=testdb -dbresource=embl -idformat=gb -directory=. -fields='id,acc,sv,des' -filenames='gbvrt*.seq' -indexoutdir=. -release=0.0 -date='00/00/00'

Then I run 'seqret' but failed to retrieve entries using 'sv' or 'des' fields:

% seqret
Reads and writes (returns) sequences
Input (gapped) sequence(s): testdb-sv:11186
Error: USA 'testdb-sv:11186' query field 'sv' not defined for database 'testdb'
Error: Unable to read sequence 'testdb-sv:11186'
Input (gapped) sequence(s): testdb-des:ribosomal
Error: USA 'testdb-des:ribosomal' query field 'des' not defined for database 'testdb'
Error: Unable to read sequence 'testdb-des:ribosomal'
Died: seqret terminated: Bad value for '-sequence' and no more retries

Even the entry does exist if I retrieve with acc number:

% seqret
Reads and writes (returns) sequences
Input (gapped) sequence(s): testdb:X67626
output sequence(s) [aa12srrna.fasta]: /scratch/out1 
%

I did tried dbiflat on this file but still have no luck with similar results.

Thank you.

Jean



From tao.song at calibrant.com  Tue Sep  5 23:54:24 2006
From: tao.song at calibrant.com (Tao Song)
Date: Tue, 5 Sep 2006 19:54:24 -0400
Subject: [EMBOSS]  protein sequence format question
Message-ID: <002101c6d146$c22442b0$1b02a8c0@tao>

Hi,

      I try to use DIGEST function in EMBOSS for tryptic digest
of protein sequence. The sequence file I download from the following 
link:
ftp://ftp.ebi.ac.uk/pub/databases/biomart/current/uniprot_mart_17/uniprot_sequence__sequence__main.txt.gz 

     It is a tab delimited flat file which includes all protein sequences. It seems
that it is not any of the formats EMBOSS support. I wonder is it still possible
to use DIGEST function?

     I attached a small file of the sequence database.

     Thanks a lot for your help!

     Regards,

     Tao     
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: protein table.txt
URL: <http://lists.open-bio.org/pipermail/emboss/attachments/20060905/a50c2348/attachment-0001.txt>

From David.Bauer at SCHERING.DE  Wed Sep  6 05:45:59 2006
From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE)
Date: Wed, 6 Sep 2006 07:45:59 +0200
Subject: [EMBOSS] Antwort:   protein sequence format question
In-Reply-To: <002101c6d146$c22442b0$1b02a8c0@tao>
Message-ID: <OFC6DF417C.78B72017-ONC12571E1.001EEC8F-C12571E1.001FAD1B@schering.de>


Hi,

the file which you try to use is a mysql dump from the biomart database.
So this is not a format which you can use with EMBOSS.
But the uniprot is also available in other formats.
Please have a look at the directory:
ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/

There you will find uniprot in fasta and embl (.dat.gz) format which can
be used with EMBOSS.
You can also index these files with the EMBOSS tools dbxfasta or dbxflat
so you can efficently retrieve individual sequences from the database.

Some more information about the sequence format supported by EMBOSS you
can find at the emboss documentation pages:
http://emboss.sourceforge.net/docs/themes/SequenceFormats.html


HTH,
David.

emboss-bounces at lists.open-bio.org schrieb am 06/09/2006 01:54:24:

> Hi,
>
>       I try to use DIGEST function in EMBOSS for tryptic digest
> of protein sequence. The sequence file I download from the following
> link:
> ftp://ftp.ebi.ac.
>
uk/pub/databases/biomart/current/uniprot_mart_17/uniprot_sequence__sequence__main.

> txt.gz
>
>      It is a tab delimited flat file which includes all protein
> sequences. It seems
> that it is not any of the formats EMBOSS support. I wonder is it
> still possible
> to use DIGEST function?



From imadnansyed at yahoo.com  Wed Sep  6 07:52:59 2006
From: imadnansyed at yahoo.com (Adnan Shahzad)
Date: Wed, 6 Sep 2006 00:52:59 -0700 (PDT)
Subject: [EMBOSS] Installing EMBOSS on SERVER
Message-ID: <20060906075259.2243.qmail@web61225.mail.yahoo.com>

Hello all,
  Well I want to run EMBOSS on my server and I want other client (pc) should access all the programs from their I am having trouble understanding how I can make client interface for the EMBOSS
.i am lost need your help.
  Thank you
  Regards,
   Adnan Shahzad


  Adnan Shahzad Research Officer Department of Bioinformatics National Centre of Excellence in Molecular Biology Lahore, Pakistan.
  web: www.cemb.edu.pk Off:- 042-5423952 Ext. 303 Cell:- 0300-5337765
   


 		
---------------------------------
Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and 30+ countries) for 2?/min or less.


From simon.andrews at bbsrc.ac.uk  Wed Sep  6 08:08:14 2006
From: simon.andrews at bbsrc.ac.uk (Simon Andrews)
Date: Wed, 6 Sep 2006 09:08:14 +0100
Subject: [EMBOSS] Installing EMBOSS on SERVER
In-Reply-To: <20060906075259.2243.qmail@web61225.mail.yahoo.com>
References: <20060906075259.2243.qmail@web61225.mail.yahoo.com>
Message-ID: <41333353-2A41-4B79-B41A-01F3783A52DC@bbsrc.ac.uk>


On 6 Sep 2006, at 08:52, Adnan Shahzad wrote:

> Hello all,
>   Well I want to run EMBOSS on my server and I want other client  
> (pc) should access all the programs from their I am having trouble  
> understanding how I can make client interface for the EMBOSS?.i am  
> lost need your help.

You have a couple of choices.

You could let everyone have an account on your server and let them  
log on to your server to run the programs directly.  Probably the  
most common way to do this would be to provide everyone with an ssh  
client to allow secure access to the server from their PCs.  We use  
putty (http://www.chiark.greenend.org.uk/~sgtatham/putty/), as our  
ssh client, but there are plenty of others.

Alternatively you could install one of the emboss web interfaces and  
a web server on your server and let everyone access the programs via  
a web browser.  Again there are a number of different interfaces  
available.  There's a list of them at http://emboss.sourceforge.net/ 
interfaces/#web.

Hope this helps

Simon.



>   Thank you
>   Regards,
>    Adnan Shahzad
>
>
>   Adnan Shahzad Research Officer Department of Bioinformatics  
> National Centre of Excellence in Molecular Biology Lahore, Pakistan.
>   web: www.cemb.edu.pk Off:- 042-5423952 Ext. 303 Cell:- 0300-5337765
>
>
>
>  		
> ---------------------------------
> Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and  
> 30+ countries) for 2?/min or less.
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss




From tao.song at calibrant.com  Wed Sep  6 13:14:02 2006
From: tao.song at calibrant.com (Tao Song)
Date: Wed, 6 Sep 2006 09:14:02 -0400
Subject: [EMBOSS] Antwort:   protein sequence format question
References: <OFC6DF417C.78B72017-ONC12571E1.001EEC8F-C12571E1.001FAD1B@schering.de>
Message-ID: <001601c6d1b6$5419d530$1b02a8c0@tao>

Hi Divad,

     Thanks so much for your help!

     Regards,

     Tao

----- Original Message ----- 
From: <David.Bauer at SCHERING.DE>
To: "Tao Song" <tao.song at calibrant.com>
Cc: <emboss at lists.open-bio.org>; <emboss-bounces at lists.open-bio.org>
Sent: Wednesday, September 06, 2006 1:45 AM
Subject: Antwort: [EMBOSS] protein sequence format question


>
> Hi,
>
> the file which you try to use is a mysql dump from the biomart database.
> So this is not a format which you can use with EMBOSS.
> But the uniprot is also available in other formats.
> Please have a look at the directory:
> ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/
>
> There you will find uniprot in fasta and embl (.dat.gz) format which can
> be used with EMBOSS.
> You can also index these files with the EMBOSS tools dbxfasta or dbxflat
> so you can efficently retrieve individual sequences from the database.
>
> Some more information about the sequence format supported by EMBOSS you
> can find at the emboss documentation pages:
> http://emboss.sourceforge.net/docs/themes/SequenceFormats.html
>
>
> HTH,
> David.
>
> emboss-bounces at lists.open-bio.org schrieb am 06/09/2006 01:54:24:
>
>> Hi,
>>
>>       I try to use DIGEST function in EMBOSS for tryptic digest
>> of protein sequence. The sequence file I download from the following
>> link:
>> ftp://ftp.ebi.ac.
>>
> uk/pub/databases/biomart/current/uniprot_mart_17/uniprot_sequence__sequence__main.
>
>> txt.gz
>>
>>      It is a tab delimited flat file which includes all protein
>> sequences. It seems
>> that it is not any of the formats EMBOSS support. I wonder is it
>> still possible
>> to use DIGEST function?
>
>
> 



From tao.song at calibrant.com  Wed Sep  6 13:27:52 2006
From: tao.song at calibrant.com (Tao Song)
Date: Wed, 6 Sep 2006 09:27:52 -0400
Subject: [EMBOSS]   protein sequence for individual species
References: <OFC6DF417C.78B72017-ONC12571E1.001EEC8F-C12571E1.001FAD1B@schering.de>
Message-ID: <001b01c6d1b8$4151def0$1b02a8c0@tao>

Hi,

    Is there a place I can download protein sequence file for individual 
species
(such as human, yeast, etc)? or is there a program can parse the big 
sequence file
into small ones for individual species?

     Sorry for so many questin. I am new to bioinformatics.

     Thanks so much for you guys' help!

     Regards,

     Tao 



From bgibbon at email.arizona.edu  Wed Sep  6 15:09:51 2006
From: bgibbon at email.arizona.edu (Bryan Gibbon)
Date: Wed, 6 Sep 2006 08:09:51 -0700
Subject: [EMBOSS] protein sequence for individual species
In-Reply-To: <001b01c6d1b8$4151def0$1b02a8c0@tao>
Message-ID: <CAEDKAEHPDBJLJLCPPAKOEGCCDAA.bgibbon@email.arizona.edu>

This can be easily done from Entrez

http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi

Just use the organism qualifier in the search command. For example to fetch
the sequences for my favorite just enter the command "Zea mays [orgn]". Then
to download the results change the display to the format you want (genbank,
fasta etc.) and use the Send to... File menu command to download the
sequences. For large data sets this can take a while but it is easy.

-----Original Message-----
From: emboss-bounces at lists.open-bio.org
[mailto:emboss-bounces at lists.open-bio.org]On Behalf Of Tao Song
Sent: Wednesday, September 06, 2006 6:28 AM
To: emboss at lists.open-bio.org; emboss-bounces at lists.open-bio.org
Subject: [EMBOSS] protein sequence for individual species


Hi,

    Is there a place I can download protein sequence file for individual
species
(such as human, yeast, etc)? or is there a program can parse the big
sequence file
into small ones for individual species?

     Sorry for so many questin. I am new to bioinformatics.

     Thanks so much for you guys' help!

     Regards,

     Tao

_______________________________________________
EMBOSS mailing list
EMBOSS at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/emboss



From d.gatherer at vir.gla.ac.uk  Thu Sep  7 07:29:19 2006
From: d.gatherer at vir.gla.ac.uk (Derek Gatherer)
Date: Thu, 07 Sep 2006 08:29:19 +0100
Subject: [EMBOSS] protein sequence for individual species
In-Reply-To: <CAEDKAEHPDBJLJLCPPAKOEGCCDAA.bgibbon@email.arizona.edu>
References: <001b01c6d1b8$4151def0$1b02a8c0@tao>
	<CAEDKAEHPDBJLJLCPPAKOEGCCDAA.bgibbon@email.arizona.edu>
Message-ID: <6.2.3.4.1.20060907082703.02ac3e88@lenzie.gla.ac.uk>

For something that has been already curated, try:

http://www.ebi.ac.uk/proteome

Cheers
Derek

At 16:09 06/09/2006, Bryan Gibbon wrote:
>This can be easily done from Entrez
>
>http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi
>
>Just use the organism qualifier in the search command. For example to fetch
>the sequences for my favorite just enter the command "Zea mays [orgn]". Then
>to download the results change the display to the format you want (genbank,
>fasta etc.) and use the Send to... File menu command to download the
>sequences. For large data sets this can take a while but it is easy.
>
>-----Original Message-----
>From: emboss-bounces at lists.open-bio.org
>[mailto:emboss-bounces at lists.open-bio.org]On Behalf Of Tao Song
>Sent: Wednesday, September 06, 2006 6:28 AM
>To: emboss at lists.open-bio.org; emboss-bounces at lists.open-bio.org
>Subject: [EMBOSS] protein sequence for individual species
>
>
>Hi,
>
>     Is there a place I can download protein sequence file for individual
>species
>(such as human, yeast, etc)? or is there a program can parse the big
>sequence file
>into small ones for individual species?
>
>      Sorry for so many questin. I am new to bioinformatics.
>
>      Thanks so much for you guys' help!
>
>      Regards,
>
>      Tao
>
>_______________________________________________
>EMBOSS mailing list
>EMBOSS at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/emboss
>
>_______________________________________________
>EMBOSS mailing list
>EMBOSS at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/emboss



From tao.song at calibrant.com  Thu Sep  7 22:27:22 2006
From: tao.song at calibrant.com (Tao Song)
Date: Thu, 7 Sep 2006 18:27:22 -0400
Subject: [EMBOSS]    iep program for multiple protein sequences
References: <CAEDKAEHPDBJLJLCPPAKOEGCCDAA.bgibbon@email.arizona.edu>
Message-ID: <002b01c6d2cc$cb4fe510$1b02a8c0@tao>

Hi,

     I wonder can the iep program  that calculates the isoelectric point of 
a protein be used
for a protein database? When asked to input protein sequence I gave 'tsw' 
instead of
'tsw:laci_ecoli' I got an error that said 'sequence must be protein sequence 
without BZ U X
or *: found bad character Z'. Does iep can only take one protein sequence as 
input file?

    I really appreciate all the help I got from you guys. Thanks a lot!

     Regards,

     Tao




From David.Bauer at SCHERING.DE  Fri Sep  8 06:28:54 2006
From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE)
Date: Fri, 8 Sep 2006 08:28:54 +0200
Subject: [EMBOSS] Antwort:     iep program for multiple protein sequences
In-Reply-To: <002b01c6d2cc$cb4fe510$1b02a8c0@tao>
Message-ID: <OF7B37072F.87038447-ONC12571E3.0022FEEC-C12571E3.00239B22@schering.de>


Hi Tao,

If you want to specify a whole database as input for iep you must use
iep tsw:\*
or
iep "tsw:*"
If you just say tsw, emboss looks for a file named tsw in the local
directory.

HTH,
David.

emboss-bounces at lists.open-bio.org schrieb am 08/09/2006 00:27:22:

> Hi,
>
>      I wonder can the iep program  that calculates the isoelectric point
of
> a protein be used
> for a protein database? When asked to input protein sequence I gave
'tsw'
> instead of
> 'tsw:laci_ecoli' I got an error that said 'sequence must be protein
sequence
> without BZ U X
> or *: found bad character Z'. Does iep can only take one protein
sequence as
> input file?
>
>     I really appreciate all the help I got from you guys. Thanks a lot!
>
>      Regards,
>
>      Tao
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss



From gbottu at ben.vub.ac.be  Fri Sep  8 07:46:32 2006
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Fri, 8 Sep 2006 09:46:32 +0200
Subject: [EMBOSS] iep program for multiple protein sequences - Checked by
In-Reply-To: <002b01c6d2cc$cb4fe510$1b02a8c0@tao>
References: <CAEDKAEHPDBJLJLCPPAKOEGCCDAA.bgibbon@email.arizona.edu>
	<002b01c6d2cc$cb4fe510$1b02a8c0@tao>
Message-ID: <20060908074632.GA22405@bigben.ulb.ac.be>

On Thu, Sep 07, 2006 at 06:27:22PM -0400, Tao Song wrote:
> I wonder can the iep program  that calculates the isoelectric point of 
> a protein be used
> for a protein database?

Yes, iep can take multiple proteins as input. It will create an output 
file with the titration curves of the different proteins the one after 
the other. It does not make one graph for all the proteins together, 
which would anyway not make much biological sence.

> When asked to input protein sequence I gave 'tsw' 
> instead of
> 'tsw:laci_ecoli' I got an error that said 'sequence must be protein sequence 
> without BZ U X
> or *: found bad character Z'. Does iep can only take one protein sequence as 
> input file?

The problem here is that iep takes as input only a protein sequence 
without ambiguity symbols. The reason is without doubt that it is not 
clear whether B should be handled as a Asp (negative) or a Asn (neutral), 
etc.

	Guy Bottu,
	Belgian EMBnet Node



From pmr at ebi.ac.uk  Fri Sep  8 11:20:24 2006
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 08 Sep 2006 12:20:24 +0100
Subject: [EMBOSS] iep program for multiple protein sequences
In-Reply-To: <002b01c6d2cc$cb4fe510$1b02a8c0@tao>
References: <CAEDKAEHPDBJLJLCPPAKOEGCCDAA.bgibbon@email.arizona.edu>
	<002b01c6d2cc$cb4fe510$1b02a8c0@tao>
Message-ID: <450151F8.5060403@ebi.ac.uk>

Tao Song wrote:
> Hi,
> 
>      I wonder can the iep program  that calculates the isoelectric point of 
> a protein be used
> for a protein database? When asked to input protein sequence I gave 'tsw' 
> instead of
> 'tsw:laci_ecoli' I got an error that said 'sequence must be protein sequence 
> without BZ U X
> or *: found bad character Z'. Does iep can only take one protein sequence as 
> input file?

Your command does read the test swissprot database, but fails on an 
entry that is a sequence fragment with a Z ambiguity code.

For the next release, I have a patch that will convert B and Z to D/N 
and E/Q using the Dayhoff frequencies of naturally occurring amino 
acids. This will convert the first B or Z to a charged residue (as these 
are more common), the second to an uncharged residue, and so on. With 
this change in place iep can be modified to accept any protein sequence 
and will produce consistent results on ambiguity codes.

A question: We can try this fix as a general solution for programs 
requiring "pureprotein" input, by converting any B or Z (or J) ambiguity 
code. Is this useful? For iep the order does not matter and the 
converted sequence does not appear in the output, but I think a 
program-by-program solution is better.

Other programs insisting on "pureprotein" input are hmoment, octanol and 
pepwindow

regards,

Peter


From imadnansyed at yahoo.com  Mon Sep 11 05:43:42 2006
From: imadnansyed at yahoo.com (Adnan Shahzad)
Date: Sun, 10 Sep 2006 22:43:42 -0700 (PDT)
Subject: [EMBOSS] EMBOSS running on server (problems)
Message-ID: <20060911054342.80134.qmail@web61220.mail.yahoo.com>

Hello Every body,
  Need your help and guidance.
  I have tried installing EMBOSS on my server with Wemboss web interface and with Apache server tomcat 5.5 but system seem to be not integrated with each other and things are not running properly.
  Kindly any one tell me any other way to keep it running which is more simpler then this one 
what about running Jemboss. 
  Can some one give me manual for step by step procedure because I am new to all this so I am doing on hit and trail bases.
  And now looking for the help from you guys.
  regards,
   


  Adnan Shahzad Research Officer Department of Bioinformatics National Centre of Excellence in Molecular Biology Lahore, Pakistan.
  web: www.cemb.edu.pk Off:- 042-5423952 Ext. 303 Cell:- 0300-5337765
   


 		
---------------------------------
 All-new Yahoo! Mail - Fire up a more powerful email and get things done faster.


From jison at ebi.ac.uk  Mon Sep 11 08:04:51 2006
From: jison at ebi.ac.uk (Jon Ison)
Date: Mon, 11 Sep 2006 09:04:51 +0100 (BST)
Subject: [EMBOSS] EMBOSS running on server (problems)
In-Reply-To: <20060911054342.80134.qmail@web61220.mail.yahoo.com>
References: <20060911054342.80134.qmail@web61220.mail.yahoo.com>
Message-ID: <1345.84.92.187.247.1157961891.squirrel@webmail.ebi.ac.uk>

Hi Adnan

For people on the list to be able to help, please be much more specific
about details of your system, what you are trying to achieve and the
problems you are having.

In the meantime, if you want a really easy way to run EMBOSS applications,
you can use one of the on-line EMBOSS Explorer (or other) servers listed here:

http://emboss.sourceforge.net/servers/

Cheers

Jon




> Hello Every body,
>   Need your help and guidance.
>   I have tried installing EMBOSS on my server with Wemboss web interface and with Apache server tomcat 5.5 but system
> seem to be not integrated with each other and things are not running properly.
>   Kindly any one tell me any other way to keep it running which is more simpler then this one 
what about running
> Jemboss.
>   Can some one give me manual for step by step procedure because I am new to all this so I am doing on hit and trail
> bases.
>   And now looking for the help from you guys.
>   regards,
>
>
>
>   Adnan Shahzad Research Officer Department of Bioinformatics National Centre of Excellence in Molecular Biology
> Lahore, Pakistan.
>   web: www.cemb.edu.pk Off:- 042-5423952 Ext. 303 Cell:- 0300-5337765
>
>
>
>
> ---------------------------------
>  All-new Yahoo! Mail - Fire up a more powerful email and get things done faster.
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>
>




From golharam at umdnj.edu  Mon Sep 11 16:28:30 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Mon, 11 Sep 2006 12:28:30 -0400
Subject: [EMBOSS] EMBOSS-Explorer Follow-up
Message-ID: <007501c6d5bf$51f63e80$2f01a8c0@GOLHARMOBILE1>

So I stepped through the code for tfm and it looks like it initially
looks in /usr/share/EMBOSS/doc/programs/html.  So 'make install' is
putting the html docs in /usr/share/EMBOSS/doc/html/emboss/apps/...  But
why?  Was this an inadvertant change?


> -----Original Message-----
> From: Ryan Golhar [mailto:golharam at umdnj.edu] 
> Sent: Monday, September 11, 2006 11:38 AM
> To: 'emboss at emboss.open-bio.org'
> Subject: EMBOSS-Explorer
> 
> 
> Does anyone know how to get a hold of Luke McCarthy?  The 
> email address I have for him is getting bounced back and he 
> hasn't responded to his sourceforge email.
> 
> Since I'm on the topic...I have two problems with 
> EMBOSS-Explorer and EMBOSS 4.0.0:
> 
> 1.  EMBOSS-Explorer uses the path of 
> /usr/share/EMBOSS/doc/programs/html, however EMBOSS html docs 
> are installed in /usr/share/EMBOSS/doc/html/emboss.  The 
> EMBASSY docs are in /usr/share/EMBOSS/doc/html/embassy.  
> 
> This seems to be completely different than where the text 
> documents are installed, /usr/share/EMBOSS/doc/programs/txt.  
> It looks like EMBOSS v3 was installing the html docs in 
> /usr/share/EMBOSS/doc/programs/html, but that has changed in v4.
> 
> So, either the EMBOSS installation needs to be told to 
> install in /usr/share/EMBOSS/doc/programs/html, or 
> EMBOSS-Explorer needs to be updated to look in 2 different 
> directories, one for EMBOSS and one for EMBASSY.
> 
> As a third option, EMBOSS-Explorer could run 'tfm -html' to 
> get the html doc generated on the fly.  This is probably 
> overkill though.
> 
> 2.  The new programs introduce new datatypes in the ACD files 
> that EMBOSS-Explorer doesn't recognize.  I get an 'unknown 
> data type' message display in my browser for these apps.
> 
> 
> --
> Ryan Golhar  -  golharam at umdnj.edu
> The Informatics Institute of UMDNJ
> 



From golharam at umdnj.edu  Mon Sep 11 15:37:39 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Mon, 11 Sep 2006 11:37:39 -0400
Subject: [EMBOSS] EMBOSS-Explorer
Message-ID: <006a01c6d5b8$372e7c90$2f01a8c0@GOLHARMOBILE1>

Does anyone know how to get a hold of Luke McCarthy?  The email address
I have for him is getting bounced back and he hasn't responded to his
sourceforge email.

Since I'm on the topic...I have two problems with EMBOSS-Explorer and
EMBOSS 4.0.0:

1.  EMBOSS-Explorer uses the path of
/usr/share/EMBOSS/doc/programs/html, however EMBOSS html docs are
installed in /usr/share/EMBOSS/doc/html/emboss.  The EMBASSY docs are in
/usr/share/EMBOSS/doc/html/embassy.  

This seems to be completely different than where the text documents are
installed, /usr/share/EMBOSS/doc/programs/txt.  It looks like EMBOSS v3
was installing the html docs in /usr/share/EMBOSS/doc/programs/html, but
that has changed in v4.

So, either the EMBOSS installation needs to be told to install in
/usr/share/EMBOSS/doc/programs/html, or EMBOSS-Explorer needs to be
updated to look in 2 different directories, one for EMBOSS and one for
EMBASSY.

As a third option, EMBOSS-Explorer could run 'tfm -html' to get the html
doc generated on the fly.  This is probably overkill though.

2.  The new programs introduce new datatypes in the ACD files that
EMBOSS-Explorer doesn't recognize.  I get an 'unknown data type' message
display in my browser for these apps.


--
Ryan Golhar  -  golharam at umdnj.edu
The Informatics Institute of UMDNJ



From pmr at ebi.ac.uk  Mon Sep 11 17:01:51 2006
From: pmr at ebi.ac.uk (Peter Rice)
Date: Mon, 11 Sep 2006 18:01:51 +0100
Subject: [EMBOSS] EMBOSS-Explorer Follow-up
In-Reply-To: <007501c6d5bf$51f63e80$2f01a8c0@GOLHARMOBILE1>
References: <007501c6d5bf$51f63e80$2f01a8c0@GOLHARMOBILE1>
Message-ID: <4505967F.7030200@ebi.ac.uk>

Ryan Golhar wrote:
> So I stepped through the code for tfm and it looks like it initially
> looks in /usr/share/EMBOSS/doc/programs/html.  So 'make install' is
> putting the html docs in /usr/share/EMBOSS/doc/html/emboss/apps/...  But
> why?  Was this an inadvertant change?

Oops. usr/share/EMBOSS/doc/html/emboss/apps/ is the new location in 
4.0.0 (so we do not have to keep copies of all the EMBASSY application 
documentation in the EMBOSS source).

Will be fixed in 4.0.0. A simple copy is one way to fix it. I will make 
a fix for tfm.

regards,

Peter


From pmr at ebi.ac.uk  Mon Sep 11 17:15:09 2006
From: pmr at ebi.ac.uk (Peter Rice)
Date: Mon, 11 Sep 2006 18:15:09 +0100
Subject: [EMBOSS] EMBOSS-Explorer Follow-up
In-Reply-To: <007501c6d5bf$51f63e80$2f01a8c0@GOLHARMOBILE1>
References: <007501c6d5bf$51f63e80$2f01a8c0@GOLHARMOBILE1>
Message-ID: <4505999D.702@ebi.ac.uk>

Ryan Golhar wrote:
> So I stepped through the code for tfm and it looks like it initially
> looks in /usr/share/EMBOSS/doc/programs/html.  So 'make install' is
> putting the html docs in /usr/share/EMBOSS/doc/html/emboss/apps/...  But
> why?  Was this an inadvertant change?

Aha ... tfm works, but tfm -html may fail.

If the program fails to find the html file, it will check the original 
distribution directory. Unfortunately, if it does find an html file ... 
it may be from version 3. I forgot about the tfm -html option when we 
moved the files.

A fix will take a few days to test. EMBASSY html documentation is not 
under the embassy package, so TFM will have to check the ACD file to 
find the EMBASSY package name. Easy enough - several other programs do 
it - but needs quite a few tests to make sure it does it correctly in 
all cases.

regards,

Peter


From andrespinzon at gmail.com  Mon Sep 11 17:05:33 2006
From: andrespinzon at gmail.com (Andres Pinzon)
Date: Mon, 11 Sep 2006 12:05:33 -0500
Subject: [EMBOSS] Fwd:  EMBOSS running on server (problems)
In-Reply-To: <8968fc7e0609111005s5eca25bbk7b4eb0bb182b67e@mail.gmail.com>
References: <20060911054342.80134.qmail@web61220.mail.yahoo.com>
	<8968fc7e0609111005s5eca25bbk7b4eb0bb182b67e@mail.gmail.com>
Message-ID: <8968fc7e0609111005y5d17c462pce98ccd3477394b5@mail.gmail.com>

---------- Forwarded message ----------
From: Andres Pinzon <andrespinzon at gmail.com>
Date: Sep 11, 2006 12:05 PM
Subject: Re: [EMBOSS] EMBOSS running on server (problems)
To: Adnan Shahzad <imadnansyed at yahoo.com>


On 9/11/06, Adnan Shahzad <imadnansyed at yahoo.com> wrote:
> Hello Every body,
>   Need your help and guidance.
>   I have tried installing EMBOSS on my server with Wemboss web interface and with Apache server tomcat 5.5 but system seem to be not integrated with each other and things are not running properly.

Hmmm... im not sure about this, but maybe it would be better if you
install wEMBOSS on an APACHE "alone" server (not tomcat). At least I
have installed wEMBOSS a couple of times without any problem.
http://bioinf.ibun.unal.edu.co/wEMBOSS/

>   Kindly any one tell me any other way to keep it running which is more simpler then this one ?what about running Jemboss.

You can run jemboss, but as a local installation and it wont be
available on internet or whatever local network you have.

>   Can some one give me manual for step by step procedure because I am new to all this so I am doing on hit and trail bases.

It depends on what interface you are willing to install. If this is
your first time, and you really need a web interface, maybe you should
try EMBOSS explorer, is pretty easy to install, BUT it lacks some good
advantages of wEMBOSS.

>   And now looking for the help from you guys.

;-)
--
Andr?s Pinz?n cPh.D.
[http://www.andrespinzon.com]
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768


-- 
Andr?s Pinz?n cPh.D.
[http://www.andrespinzon.com]
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768



From andrespinzon at gmail.com  Mon Sep 11 17:22:32 2006
From: andrespinzon at gmail.com (Andres Pinzon)
Date: Mon, 11 Sep 2006 12:22:32 -0500
Subject: [EMBOSS] EMBOSS-Explorer
In-Reply-To: <007701c6d5c7$1379dec0$2f01a8c0@GOLHARMOBILE1>
References: <8968fc7e0609111008u1fb383edo11e0bc3719acc699@mail.gmail.com>
	<007701c6d5c7$1379dec0$2f01a8c0@GOLHARMOBILE1>
Message-ID: <8968fc7e0609111022t6d8f0691ub54d2b7e2d38c8a9@mail.gmail.com>

On 9/11/06, Ryan Golhar <golharam at umdnj.edu> wrote:
> But that doesn't help EMBASSY packages
yep, you are right I just noticed it . Excuse me. ;-)
>
> > -----Original Message-----
> > From: Andres Pinzon [mailto:andrespinzon at gmail.com]
> > Sent: Monday, September 11, 2006 1:08 PM
> > To: golharam at umdnj.edu
> > Subject: Re: [EMBOSS] EMBOSS-Explorer
> >
> >
> > On 9/11/06, Ryan Golhar <golharam at umdnj.edu> wrote:
> > > Does anyone know how to get a hold of Luke McCarthy?  The email
> > > address I have for him is getting bounced back and he
> > hasn't responded
> > > to his sourceforge email.
> > >
> > > Since I'm on the topic...I have two problems with
> > EMBOSS-Explorer and
> > > EMBOSS 4.0.0:
> > >
> > > 1.  EMBOSS-Explorer uses the path of
> > > /usr/share/EMBOSS/doc/programs/html, however EMBOSS html docs are
> > > installed in /usr/share/EMBOSS/doc/html/emboss.  The
> > EMBASSY docs are
> > > in /usr/share/EMBOSS/doc/html/embassy.
> >
> > Just make a symlink. It works for me ;-) check it out:
> > http://bioinf.ibun.unal.edu.co/eexplorer/
> > --
> > Andr?s Pinz?n
> > cPh.D.
> > [http://www.andrespinzon.com]
> > Bioinformatics Center, Colombia EMBnet node
> > http://bioinf.ibun.unal.edu.co Tel +57 3165000 > ext 16961 Fax
> > +571 3165415 Micology and Phytopathology Laboratory - Los
> > Andes University. Tel +571 3394949 ext. 2768
> >
>
>


-- 
Andr?s Pinz?n cPh.D.
[http://www.andrespinzon.com]
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768



From andrespinzon at gmail.com  Mon Sep 11 17:08:21 2006
From: andrespinzon at gmail.com (Andres Pinzon)
Date: Mon, 11 Sep 2006 12:08:21 -0500
Subject: [EMBOSS] Fwd:  EMBOSS-Explorer
In-Reply-To: <8968fc7e0609111008u1fb383edo11e0bc3719acc699@mail.gmail.com>
References: <006a01c6d5b8$372e7c90$2f01a8c0@GOLHARMOBILE1>
	<8968fc7e0609111008u1fb383edo11e0bc3719acc699@mail.gmail.com>
Message-ID: <8968fc7e0609111008k496447f0o7f40a2d2002be8b2@mail.gmail.com>

---------- Forwarded message ----------
From: Andres Pinzon <andrespinzon at gmail.com>
Date: Sep 11, 2006 12:08 PM
Subject: Re: [EMBOSS] EMBOSS-Explorer
To: golharam at umdnj.edu


On 9/11/06, Ryan Golhar <golharam at umdnj.edu> wrote:
> Does anyone know how to get a hold of Luke McCarthy?  The email address
> I have for him is getting bounced back and he hasn't responded to his
> sourceforge email.
>
> Since I'm on the topic...I have two problems with EMBOSS-Explorer and
> EMBOSS 4.0.0:
>
> 1.  EMBOSS-Explorer uses the path of
> /usr/share/EMBOSS/doc/programs/html, however EMBOSS html docs are
> installed in /usr/share/EMBOSS/doc/html/emboss.  The EMBASSY docs are in
> /usr/share/EMBOSS/doc/html/embassy.

Just make a symlink. It works for me ;-) check it out:
http://bioinf.ibun.unal.edu.co/eexplorer/
--
Andr?s Pinz?n cPh.D.
[http://www.andrespinzon.com]
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768


-- 
Andr?s Pinz?n cPh.D.
[http://www.andrespinzon.com]
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768



From golharam at umdnj.edu  Mon Sep 11 17:11:35 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Mon, 11 Sep 2006 13:11:35 -0400
Subject: [EMBOSS] EMBOSS-Explorer Follow-up
In-Reply-To: <4505967F.7030200@ebi.ac.uk>
Message-ID: <007601c6d5c5$56589f80$2f01a8c0@GOLHARMOBILE1>

Okay thanks.  Then I think maybe EMBOSS-Explorer should do a 'tfm -html
<appname>'.  That would make it independent of the EMBOSS version and
rely on tfm to generate the html documentation.  I'll play around with
that change.  Do you know how to get a hold of Luke btw?

Ryan


> -----Original Message-----
> From: Peter Rice [mailto:pmr at ebi.ac.uk] 
> Sent: Monday, September 11, 2006 1:02 PM
> To: golharam at umdnj.edu
> Cc: emboss at emboss.open-bio.org
> Subject: Re: [EMBOSS] EMBOSS-Explorer Follow-up
> 
> 
> Ryan Golhar wrote:
> > So I stepped through the code for tfm and it looks like it 
> initially 
> > looks in /usr/share/EMBOSS/doc/programs/html.  So 'make install' is 
> > putting the html docs in 
> /usr/share/EMBOSS/doc/html/emboss/apps/...  
> > But why?  Was this an inadvertant change?
> 
> Oops. usr/share/EMBOSS/doc/html/emboss/apps/ is the new location in 
> 4.0.0 (so we do not have to keep copies of all the EMBASSY 
> application 
> documentation in the EMBOSS source).
> 
> Will be fixed in 4.0.0. A simple copy is one way to fix it. I 
> will make 
> a fix for tfm.
> 
> regards,
> 
> Peter
> 



From golharam at umdnj.edu  Mon Sep 11 18:37:53 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Mon, 11 Sep 2006 14:37:53 -0400
Subject: [EMBOSS] EMBOSS-Explorer Follow-up
In-Reply-To: <416B9A34D7CA1C4C9ED58354E75101BBA3815B@NIHCESMLBX3.nih.gov>
Message-ID: <007b01c6d5d1$653d38b0$2f01a8c0@GOLHARMOBILE1>

Yes, I tried that, but it doesn't work for EMBASSY applications as they
fall in /usr/share/EMBOSS/doc/html/embassy/apps/...

> -----Original Message-----
> From: Mao, Jean (NIH/CIT) [E] [mailto:maoj at mail.nih.gov] 
> Sent: Monday, September 11, 2006 2:28 PM
> To: golharam at umdnj.edu
> Cc: emboss at emboss.open-bio.org
> Subject: RE: [EMBOSS] EMBOSS-Explorer Follow-up
> 
> 
> Have you tried to modify the Conf.pm page? It's under our 
> /usr/local/perl-5.8.7/lib/site_perl/5.8.7/EMBOSS/GUI/Conf.pm 
> and just modify the line to the right directory for the 
> manual html pages. I did and it worked. Luke's email is  
> 'mccarthy at users.sourceforge.net'
> 
> -----Original Message-----
> From: Ryan Golhar [mailto:golharam at umdnj.edu] 
> Sent: Monday, September 11, 2006 1:12 PM
> To: 'Peter Rice'
> Cc: emboss at emboss.open-bio.org
> Subject: Re: [EMBOSS] EMBOSS-Explorer Follow-up
> 
> Okay thanks.  Then I think maybe EMBOSS-Explorer should do a 
> 'tfm -html <appname>'.  That would make it independent of the 
> EMBOSS version and rely on tfm to generate the html 
> documentation.  I'll play around with that change.  Do you 
> know how to get a hold of Luke btw?
> 
> Ryan
> 
> 
> > -----Original Message-----
> > From: Peter Rice [mailto:pmr at ebi.ac.uk]
> > Sent: Monday, September 11, 2006 1:02 PM
> > To: golharam at umdnj.edu
> > Cc: emboss at emboss.open-bio.org
> > Subject: Re: [EMBOSS] EMBOSS-Explorer Follow-up
> > 
> > 
> > Ryan Golhar wrote:
> > > So I stepped through the code for tfm and it looks like it
> > initially
> > > looks in /usr/share/EMBOSS/doc/programs/html.  So 'make 
> install' is
> > > putting the html docs in
> > /usr/share/EMBOSS/doc/html/emboss/apps/...
> > > But why?  Was this an inadvertant change?
> > 
> > Oops. usr/share/EMBOSS/doc/html/emboss/apps/ is the new location in
> > 4.0.0 (so we do not have to keep copies of all the EMBASSY 
> application 
> > documentation in the EMBOSS source).
> > 
> > Will be fixed in 4.0.0. A simple copy is one way to fix it. I will
> > make a fix for tfm.
> > 
> > regards,
> > 
> > Peter
> > 
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org 
> http://lists.open-> bio.org/mailman/listinfo/emboss
> 



From andrespinzon at gmail.com  Tue Sep 12 14:31:08 2006
From: andrespinzon at gmail.com (Andres Pinzon)
Date: Tue, 12 Sep 2006 09:31:08 -0500
Subject: [EMBOSS] EMBOSS running on server (problems)
In-Reply-To: <20060912045707.53921.qmail@web61222.mail.yahoo.com>
References: <8968fc7e0609111005y5d17c462pce98ccd3477394b5@mail.gmail.com>
	<20060912045707.53921.qmail@web61222.mail.yahoo.com>
Message-ID: <8968fc7e0609120731sdc10dd7k7dc86b7bb185aad6@mail.gmail.com>

On 9/11/06, Adnan Shahzad <imadnansyed at yahoo.com> wrote:
>
>
> Hello Andres\
Hi Adnan! Im replying to you as well as to the whole list, maybe this
thread could be helpful for someone, sometime.

> For installing this I need following things right
>
> 1)       EMBOSS
> 2)       Web Server
> 3)       WEMBOSS
> Right

Yep, thats it.

> So when u installed the wemboss you took guidline from its "read me file" or
> you have to use some modification because I am getting some directory error
> for this that is

Yep, I just used that file.

>
> the location of /cgi_bin/ in the file system. I have added the appropriate
> entry in httpd.conf file as said in README file.
> But the server still responds a file not found ERROR.

Ok, by default cgi-bin is a directory above the webroot on your apache
installation.

>
> What should be the location of   /wEMBOSS_cgi/ in the hierarchy of the
> server?

What I did was not to use the apache's cgi-bin default directory but a
wEMBOSS_cgi:  /whatever/wEMBOSS/cgi-bin  and defined this directory as
executable in the httpd.conf file.
It should look like this:
##########################################
ScriptAlias /wEMBOSS_cgi/    "/whatever/wEMBOSS/cgi-bin"

<Directory "/whatever/wEMBOSS/cgi-bin">
Authtype basic
AuthUserFile "/etc/shadow"
require valid-user
Order allow,deny
</directory>
Allow from all
###############################

Please take into account that AuthUserFile can have different methods,
this is just an example, but it should work. In this case what you are
telling to the system is that wemboss will be accesed only for those
users that are valid system users too.
>
> Operating system that I am using is  Linux.

GNU/Linux... cool!

Hope this helps.
-- 
Andr?s Pinz?n cPh.D.
[http://www.andrespinzon.com]
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768



From imadnansyed at yahoo.com  Wed Sep 13 05:59:35 2006
From: imadnansyed at yahoo.com (Adnan Shahzad)
Date: Tue, 12 Sep 2006 22:59:35 -0700 (PDT)
Subject: [EMBOSS] EMBOSS running on server (problems)
In-Reply-To: <20060911160341.GA3050@bigben.ulb.ac.be>
Message-ID: <20060913055935.44143.qmail@web61211.mail.yahoo.com>

Hello Guy Bottu,
  i have cheacked and corrected and now i am getting this error when i run the Wemboss that is 
  " Sorry the owner of the this process is not allowed to run the catch program ask wemboss manager"
   
  i am login and using as admin.
  Kindly need your wise thoughts on it.
   
  Regards
   
  

Guy Bottu <gbottu at ben.vub.ac.be> wrote:
  On Mon, Sep 11, 2006 at 02:02:49AM -0700, Adnan Shahzad wrote:
> My problem is that , 
> the location of /cgi_bin/ in the file system. I have added the appropriate entry in httpd.conf file as said in README file.
> But the server still responds a file not found ERROR.
> 
> What should be the location of /wEMBOSS_cgi/ in the hierarchy of the server?
> 

Your file httpd.conf should contain something as :


ScriptAlias /wEMBOSS_cgi/ /XXX/wEMBOSS/cgi-bin/


AllowOverride None
Options +ExecCGI -Includes
Order allow,deny
Allow from all
AuthType basic
AuthUserFile "/etc/shadow"
Authname 'YYY'
require valid-user



where /XXX/wEMBOSS/cgi-bin is a directory containing catch and emboss.pl.
Note that catch must be setuid :
-rwsr-xr-x 1 root root 12941 2006-09-02 10:47 catch

Instead of /etc/shadow you can have /etc/passwd or whatever file contains 
the user passwords

YYY is a name of a categrory of users (e.g. EMBOSS user) ; it ca, be 
shared with other applications protected by password.

Does that correspond to what you have ?

Guy





  Adnan Shahzad Research Officer Department of Bioinformatics National Centre of Excellence in Molecular Biology Lahore, Pakistan.
  web: www.cemb.edu.pk Off:- 042-5423952 Ext. 303 Cell:- 0300-5337765
   


 		
---------------------------------
 All-new Yahoo! Mail - Fire up a more powerful email and get things done faster.


From neil.brookes at cancer.org.uk  Wed Sep 13 10:19:30 2006
From: neil.brookes at cancer.org.uk (Neil Brookes)
Date: Wed, 13 Sep 2006 11:19:30 +0100
Subject: [EMBOSS] Jemboss problems with fuzzpro and fuzznuc
Message-ID: <4507DB32.7040903@cancer.org.uk>

Hi,

I think I have unearthed an issue with fuzzpro/fuzznuz and EMBOSS 4.0.0
The old version in 3.0.0 had a '-mismatch' option. This has changed in 
version 4.0.0 to '-pmismatch'.

The 'mismatch' integer element seems to have been removed from the 
fuzzpro/nuc ACD files.
I'm not sure how/when Jemboss parses the ACD flies, but it doesn't seem 
to be allowing for the  new '-pmismatch' option, and users are unable to 
specify a value.

any ideas ?

cheers
Neil

-- 
Neil Brookes
Bioinformatics
Cancer Research UK

+ 44 (0)207 2693063



From charles-listes-emboss at plessy.org  Thu Sep 14 15:07:36 2006
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Fri, 15 Sep 2006 00:07:36 +0900
Subject: [EMBOSS] Building EMBOSS with an external libpcre.
Message-ID: <20060914150736.GD1510@kunpuu.plessy.org>

Dear developpers,

I am preparing Debian packages for EMBOSS, and I run in the following
problem:

EMBOSS is shipped and built with its own copy of libpcre. As a result,
the EMBOSS Debian package contains some files wich are also in the
libpcre Debian package, and they conflict together.

I could remove the conflicting files from the EMBOSS package, but I
think that it is unwise, as the libpcre in Debian does not have the same
version number.

It would be much cleaner if I could build EMBOSS with the libpcre from
Debian, but I could not figure out how to do. Can somebody give me
hints?

Have a nice day,

-- 
Charles Plessy
Debian-Med packaging team
http://www.debian.org/devel/debian-med/


From Suraj.Mukatira at STJUDE.ORG  Thu Sep 14 16:14:17 2006
From: Suraj.Mukatira at STJUDE.ORG (Mukatira, Suraj)
Date: Thu, 14 Sep 2006 11:14:17 -0500
Subject: [EMBOSS] installing EMBOSS-4.0.0 in ubuntu
Message-ID: <F2235647AC878D438F09255C39842FBC1563A319@SJMEMXMB03.stjude.sjcrh.local>


Hello there,
After configure and running 'make' I get the following error (at the
end):

/usr/bin/ld: cannot find -lX11
Collect2: ld returned to exit status
make[2]: *** [aaindexextract] error 1
make[1]: *** [check-recursive] error 1

under /usr/bin/ld I do have X11 and my xterm works just fine.

After running 'make install' I notice similar errors as above.

Bottom line emboss does not run on my machine...

Help!


Suraj Mukatira




From anoop.rajendra at gmail.com  Thu Sep 14 17:24:22 2006
From: anoop.rajendra at gmail.com (Anoop Rajendra)
Date: Thu, 14 Sep 2006 10:24:22 -0700
Subject: [EMBOSS] installing EMBOSS-4.0.0 in ubuntu
In-Reply-To: <F2235647AC878D438F09255C39842FBC1563A319@SJMEMXMB03.stjude.sjcrh.local>
References: <F2235647AC878D438F09255C39842FBC1563A319@SJMEMXMB03.stjude.sjcrh.local>
Message-ID: <E768DD8D-CAD6-4B25-95AE-15728D25E488@gmail.com>

You need the X11 devel packages. On Ubuntu, I believe they are named  
xorg-x11-devel (or permutations thereof).

-anoop

On Sep 14, 2006, at 9:14 AM, Mukatira, Suraj wrote:

>
> Hello there,
> After configure and running 'make' I get the following error (at the
> end):
>
> /usr/bin/ld: cannot find -lX11
> Collect2: ld returned to exit status
> make[2]: *** [aaindexextract] error 1
> make[1]: *** [check-recursive] error 1
>
> under /usr/bin/ld I do have X11 and my xterm works just fine.
>
> After running 'make install' I notice similar errors as above.
>
> Bottom line emboss does not run on my machine...
>
> Help!
>
>
> Suraj Mukatira
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss



From charles-listes-emboss at plessy.org  Fri Sep 15 00:38:24 2006
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Fri, 15 Sep 2006 09:38:24 +0900
Subject: [EMBOSS] installing EMBOSS-4.0.0 in ubuntu
In-Reply-To: <E768DD8D-CAD6-4B25-95AE-15728D25E488@gmail.com>
References: <F2235647AC878D438F09255C39842FBC1563A319@SJMEMXMB03.stjude.sjcrh.local>
	<E768DD8D-CAD6-4B25-95AE-15728D25E488@gmail.com>
Message-ID: <20060915003824.GB10859@kunpuu.plessy.org>

Le Thu, Sep 14, 2006 at 10:24:22AM -0700, Anoop Rajendra a ?crit :
> You need the X11 devel packages. On Ubuntu, I believe they are named  
> xorg-x11-devel (or permutations thereof).

Hi all,

On Debian systems, I think that the following packages have to be
installed in order to builid EMBOSS (the first two being related to X).
It should not be very different on an Ubuntu system, as it is based on
Debian.

libx11-dev, x-dev, libgdchart-gd2-xpm-dev, zlib1g-dev, libpng12-dev

Good luck,

-- 
Charles Plessy
Debian-Med packaging team
http://www.debian.org/devel/debian-med/


From imadnansyed at yahoo.com  Fri Sep 15 12:29:46 2006
From: imadnansyed at yahoo.com (Adnan Shahzad)
Date: Fri, 15 Sep 2006 05:29:46 -0700 (PDT)
Subject: [EMBOSS] EMBOSS running on server (problems)
In-Reply-To: <20060913080756.GA24935@bigben.ulb.ac.be>
Message-ID: <20060915122946.30996.qmail@web61221.mail.yahoo.com>

Hello Guy Bottu,
  well i am again ending up in more issue and now this time as you said 
  in my "httpd.conf" the command was 
  user Apache
  and 
  group Apache
  i have replace Apache with nobody which i used in catch.c file.
   
  but now its giving me this error 
   
  "Internal Server Error
  The server encountered an internal error or misconfiguration and was unable to complete your request.
  Please contact the server administrator, root at localhost and inform them of the time the error occurred, and anything you might have done that may have caused the error.
  More information about this error may be available in the server error log.
   
  one more thing if i run from Windows Browser what should be my login on the win DOMAIN.
   
  Help me out buddy
  Regards,
   
  
---------------------------------
       

Guy Bottu <gbottu at ben.vub.ac.be> wrote:
  
Take a look at the file catch.c in the installation directory. It 
contains a line :
#define NOBODY "XXX"
In httpd.conf or maybe some other file in the configuration of your WWW 
server there should be a line :
User XXX
Both should match. XXX is the name of the user that is running the WWW 
server. Usually it is "root" that starts up the httpd demon, but then the 
program shifts user to a user "www", "nobody" or whatever, who has 
limited rights, e.g. not the right to run a shell. The wEMBOSS master 
program catch checks whether it has been started by the user who is 
running the httpd server and then shifts to the user who typed in his 
username+password ; if catch has been started by another user, it exits 
with the error message you saw. All this is for evident security reasons.

The wEMBOSS installation script asks you which user is running the WWW 
server. Try to figure out who that user is and run the installation 
script again.

Guy




  Adnan Shahzad Research Officer Department of Bioinformatics National Centre of Excellence in Molecular Biology Lahore, Pakistan.
  web: www.cemb.edu.pk Off:- 042-5423952 Ext. 303 Cell:- 0300-5337765
   


 		
---------------------------------
Stay in the know. Pulse on the new Yahoo.com.  Check it out. 


From imadnansyed at yahoo.com  Sat Sep 16 04:23:47 2006
From: imadnansyed at yahoo.com (Adnan Shahzad)
Date: Fri, 15 Sep 2006 21:23:47 -0700 (PDT)
Subject: [EMBOSS] EMBOSS running on server (problems)
In-Reply-To: <20060915181224.GA25610@bigben.ulb.ac.be>
Message-ID: <20060916042347.52345.qmail@web61213.mail.yahoo.com>

Hello Guy and every one
  well yes i checked in the log file and it gives one very strange error which i am not able to understand and that is...in the log file it gives me this error 
   
  Premature end of script headers: catch, referer: http://linwin/wEMBOSS/wEMBOSS.html
  
any thoughts on this
   
  Regards
Guy Bottu <gbottu at ben.vub.ac.be> wrote:
  On Fri, Sep 15, 2006 at 05:29:46AM -0700, Adnan Shahzad wrote:
> but now its giving me this error 
> 
> "Internal Server Error
> The server encountered an internal error or misconfiguration and was unable to complete your request.
> Please contact the server administrator, root at localhost and inform them of the time the error occurred, and anything you might have done that may have caused the error.
> More information about this error may be available in the server error log.

Oops, it is becoming tricky now. One possible way to diagnose the problem 
is to, as the message suggests, look in the error_log file of Apache and 
see what lines related to wEMBOSS say.



  Adnan Shahzad Research Officer Department of Bioinformatics National Centre of Excellence in Molecular Biology Lahore, Pakistan.
  web: www.cemb.edu.pk Off:- 042-5423952 Ext. 303 Cell:- 0300-5337765
   


 			
---------------------------------
Get your own web address for just $1.99/1st yr. We'll help. Yahoo! Small Business.


From imadnansyed at yahoo.com  Sat Sep 16 09:29:33 2006
From: imadnansyed at yahoo.com (Adnan Shahzad)
Date: Sat, 16 Sep 2006 02:29:33 -0700 (PDT)
Subject: [EMBOSS] Jemboss help
Message-ID: <20060916092933.23943.qmail@web61225.mail.yahoo.com>

Hello every body,
   
  can any one  please tell me that in the Jemboss when you install it. it says to install Jemboss run the "installer script" i am unable to find that script can you tell me how to get hold of that.
  Regards,


  Adnan Shahzad Research Officer Department of Bioinformatics National Centre of Excellence in Molecular Biology Lahore, Pakistan.
  web: www.cemb.edu.pk Off:- 042-5423952 Ext. 303 Cell:- 0300-5337765
   


 		
---------------------------------
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From imadnansyed at yahoo.com  Mon Sep 18 12:30:55 2006
From: imadnansyed at yahoo.com (Adnan Shahzad)
Date: Mon, 18 Sep 2006 05:30:55 -0700 (PDT)
Subject: [EMBOSS] EMBOSS EXPLORER help
Message-ID: <20060918123055.78267.qmail@web61221.mail.yahoo.com>

Hello every one 
  I have installed EMBOSS EXPLORER but the issue is that how to run it in the in the explorer. Their is nothing written in Read me file so any wise thoughts on that.
  Regards
   
   
   
     



  Adnan Shahzad Research Officer Department of Bioinformatics National Centre of Excellence in Molecular Biology Lahore, Pakistan.
  web: www.cemb.edu.pk Off:- 042-5423952 Ext. 303 Cell:- 0300-5337765
   


 		
---------------------------------
How low will we go? Check out Yahoo! Messenger?s low  PC-to-Phone call rates.


From abhishek.vit at gmail.com  Mon Sep 18 16:22:31 2006
From: abhishek.vit at gmail.com (Abhishek Pratap)
Date: Mon, 18 Sep 2006 21:52:31 +0530
Subject: [EMBOSS] Problem Installing Jemboss
Message-ID: <be9b52410609180922j602e1f40le2aa0444ff20fa5@mail.gmail.com>

I am unable to install jemboss on solaris 10. with all the dependencies
installed (png, gd etc) i am getting this error.


This is the error i get each

------------------------- WARNING ----------------------------

The script has detected that /usr/include/gd.h
does not exist

Download gd from
       http://www.boutell.com/gd/

For details see the EMBOSS admin guide:
http://emboss.sourceforge.net/admin/

To exit use Control C or press return to continue.

--------------------------------------------------------------



>>>>>
the gd.h file is allready present in the /usr/include

Can someone guide me  on this

-- 
-----------------------------
Abhishek Pratap
Third Year
Bioinformatics
School of Biotechnology & Chemical Eng
VIT
Vellore.
INDIA
Ph:   (91)-416-3206020
Mob: (91)-9843181010


From andrespinzon at gmail.com  Mon Sep 18 17:22:24 2006
From: andrespinzon at gmail.com (Andres Pinzon)
Date: Mon, 18 Sep 2006 12:22:24 -0500
Subject: [EMBOSS] Fwd:  EMBOSS EXPLORER help
In-Reply-To: <8968fc7e0609181022l64359803l3084ba64a8474cba@mail.gmail.com>
References: <20060918123055.78267.qmail@web61221.mail.yahoo.com>
	<8968fc7e0609181022l64359803l3084ba64a8474cba@mail.gmail.com>
Message-ID: <8968fc7e0609181022l5e83c918h87bc87d02ebc292c@mail.gmail.com>

---------- Forwarded message ----------
From: Andres Pinzon <andrespinzon at gmail.com>
Date: Sep 18, 2006 12:22 PM
Subject: Re: [EMBOSS] EMBOSS EXPLORER help
To: Adnan Shahzad <imadnansyed at yahoo.com>


On 9/18/06, Adnan Shahzad <imadnansyed at yahoo.com> wrote:
> Hello every one
>   I have installed EMBOSS EXPLORER but the issue is that how to run it in the in the explorer. Their is nothing written in Read me file so any wise thoughts on that.

hmmm... your problem is not is not complete clear for me but...
Where did you installed it? It should be somewhere in your webserver
document root, so you can acces iit typing the following:
http://localhost/INSTALL_DIR/

just change INSTALL_DIR for the actual name of the emboss explorer
installation dir. If it was installed in an user space the following
could help:
http://localhost/~USERNAME/

Of course, change user name for the user who did the installation.

--
Andr?s Pinz?n cPh.D.
[http://www.andrespinzon.com]
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768


-- 
Andr?s Pinz?n cPh.D.
[http://www.andrespinzon.com]
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
Tel +571 3394949 ext. 2768



From Suraj.Mukatira at STJUDE.ORG  Mon Sep 18 19:54:21 2006
From: Suraj.Mukatira at STJUDE.ORG (Mukatira, Suraj)
Date: Mon, 18 Sep 2006 14:54:21 -0500
Subject: [EMBOSS] EMBOSS EXPLORER installation help
Message-ID: <F2235647AC878D438F09255C39842FBC157626B5@SJMEMXMB03.stjude.sjcrh.local>

Hi all,
I have questions regarding emboss explorer installation. Attached is the
explorer configuration file

I have emboss4.0 running in my linux machine: /usr/local/bin and
/var/www/emboss

After following instructions on the emboss explorer installation I
cannot see the webpage:
Not Found
The requested URL /cgi-bin/emboss/intro was not found on this server.

Not Found
The requested URL /cgi-bin/emboss/menu was not found on this server

Here are some directory structures:

drwxrwxr-x  2 mukatira mukatira   4096 2006-09-15 14:02 cgi-bin
drwxr-xr-x  6 mukatira mukatira   4096 2006-09-18 13:58 emboss
drwxrwxr-x  3 mukatira mukatira   4096 2006-09-15 14:02 html
-rw-r--r--  1 mukatira mukatira   1457 2006-09-11 14:28 index.html
$>:/var/www$ pwd
/var/www

Under cgi-bin I do not see a folder 'emboss'

$>/var/www/cgi-bin$ ls -l
-rwxrwxr-x 1 root root 110 2006-09-18 14:34 emboss
$>:/var/www/cgi-bin$ more emboss
#!/usr/bin/perl

use strict;
use warnings;

use EMBOSS::GUI;

my $emboss = EMBOSS::GUI->new();
$emboss->go();




Thanks in anticipation.
Also, what is the best way to completely uninstall emboss. 
-------------- next part --------------
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From golharam at umdnj.edu  Mon Sep 18 21:42:03 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Mon, 18 Sep 2006 17:42:03 -0400
Subject: [EMBOSS] EMBOSS EXPLORER installation help
In-Reply-To: <F2235647AC878D438F09255C39842FBC157626B5@SJMEMXMB03.stjude.sjcrh.local>
Message-ID: <016a01c6db6b$4abd4760$2f01a8c0@GOLHARMOBILE1>

Where there any errors from the install script you ran?  

Are you able to see your main page?  http://<servername>/cgi-bin/emboss?



> -----Original Message-----
> From: emboss-bounces at lists.open-bio.org 
> [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of 
> Mukatira, Suraj
> Sent: Monday, September 18, 2006 3:54 PM
> To: emboss at emboss.open-bio.org
> Subject: [EMBOSS] EMBOSS EXPLORER installation help
> 
> 
> Hi all,
> I have questions regarding emboss explorer installation. 
> Attached is the explorer configuration file
> 
> I have emboss4.0 running in my linux machine: /usr/local/bin 
> and /var/www/emboss
> 
> After following instructions on the emboss explorer 
> installation I cannot see the webpage: Not Found The 
> requested URL /cgi-bin/emboss/intro was not found on this server.
> 
> Not Found
> The requested URL /cgi-bin/emboss/menu was not found on this server
> 
> Here are some directory structures:
> 
> drwxrwxr-x  2 mukatira mukatira   4096 2006-09-15 14:02 cgi-bin
> drwxr-xr-x  6 mukatira mukatira   4096 2006-09-18 13:58 emboss
> drwxrwxr-x  3 mukatira mukatira   4096 2006-09-15 14:02 html
> -rw-r--r--  1 mukatira mukatira   1457 2006-09-11 14:28 index.html
> $>:/var/www$ pwd
> /var/www
> 
> Under cgi-bin I do not see a folder 'emboss'
> 
> $>/var/www/cgi-bin$ ls -l
> -rwxrwxr-x 1 root root 110 2006-09-18 14:34 emboss 
> $>:/var/www/cgi-bin$ more emboss #!/usr/bin/perl
> 
> use strict;
> use warnings;
> 
> use EMBOSS::GUI;
> 
> my $emboss = EMBOSS::GUI->new();
> $emboss->go();
> 
> 
> 
> 
> Thanks in anticipation.
> Also, what is the best way to completely uninstall emboss. 
> 



From Suraj.Mukatira at STJUDE.ORG  Mon Sep 18 21:42:57 2006
From: Suraj.Mukatira at STJUDE.ORG (Mukatira, Suraj)
Date: Mon, 18 Sep 2006 16:42:57 -0500
Subject: [EMBOSS] EMBOSS EXPLORER installation help.    .
Message-ID: <F2235647AC878D438F09255C39842FBC157627EB@SJMEMXMB03.stjude.sjcrh.local>


No.

http://10.1.6.145/cgi-bin/emboss/

Not Found
The requested URL /cgi-bin/emboss/ was not found on this server.

-----Original Message-----
From: Ryan Golhar [mailto:golharam at umdnj.edu] 
Sent: Monday, September 18, 2006 4:42 PM
To: Mukatira, Suraj
Cc: emboss at emboss.open-bio.org
Subject: RE: [EMBOSS] EMBOSS EXPLORER installation help. .

Where there any errors from the install script you ran?  

Are you able to see your main page?  http://<servername>/cgi-bin/emboss?



> -----Original Message-----
> From: emboss-bounces at lists.open-bio.org 
> [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of 
> Mukatira, Suraj
> Sent: Monday, September 18, 2006 3:54 PM
> To: emboss at emboss.open-bio.org
> Subject: [EMBOSS] EMBOSS EXPLORER installation help
> 
> 
> Hi all,
> I have questions regarding emboss explorer installation. 
> Attached is the explorer configuration file
> 
> I have emboss4.0 running in my linux machine: /usr/local/bin 
> and /var/www/emboss
> 
> After following instructions on the emboss explorer 
> installation I cannot see the webpage: Not Found The 
> requested URL /cgi-bin/emboss/intro was not found on this server.
> 
> Not Found
> The requested URL /cgi-bin/emboss/menu was not found on this server
> 
> Here are some directory structures:
> 
> drwxrwxr-x  2 mukatira mukatira   4096 2006-09-15 14:02 cgi-bin
> drwxr-xr-x  6 mukatira mukatira   4096 2006-09-18 13:58 emboss
> drwxrwxr-x  3 mukatira mukatira   4096 2006-09-15 14:02 html
> -rw-r--r--  1 mukatira mukatira   1457 2006-09-11 14:28 index.html
> $>:/var/www$ pwd
> /var/www
> 
> Under cgi-bin I do not see a folder 'emboss'
> 
> $>/var/www/cgi-bin$ ls -l
> -rwxrwxr-x 1 root root 110 2006-09-18 14:34 emboss 
> $>:/var/www/cgi-bin$ more emboss #!/usr/bin/perl
> 
> use strict;
> use warnings;
> 
> use EMBOSS::GUI;
> 
> my $emboss = EMBOSS::GUI->new();
> $emboss->go();
> 
> 
> 
> 
> Thanks in anticipation.
> Also, what is the best way to completely uninstall emboss. 
> 






From golharam at umdnj.edu  Mon Sep 18 21:58:40 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Mon, 18 Sep 2006 17:58:40 -0400
Subject: [EMBOSS] EMBOSS EXPLORER installation help.    .
In-Reply-To: <F2235647AC878D438F09255C39842FBC157627EB@SJMEMXMB03.stjude.sjcrh.local>
Message-ID: <016e01c6db6d$9d61d330$2f01a8c0@GOLHARMOBILE1>

Sounds like something is wrong with your cgi handler.  Are you able to
execute any cgi scripts in cgi-bin?  If not, can you include a copy of
your httpd.conf file and the error from /var/log/httpd/error_log?


> -----Original Message-----
> From: Mukatira, Suraj [mailto:Suraj.Mukatira at stjude.org] 
> Sent: Monday, September 18, 2006 5:43 PM
> To: golharam at umdnj.edu
> Cc: emboss at emboss.open-bio.org
> Subject: RE: [EMBOSS] EMBOSS EXPLORER installation help. .
> 
> 
> 
> No.
> 
> http://10.1.6.145/cgi-bin/emboss/
> 
> Not Found
> The requested URL /cgi-bin/emboss/ was not found on this server.
> 
> -----Original Message-----
> From: Ryan Golhar [mailto:golharam at umdnj.edu] 
> Sent: Monday, September 18, 2006 4:42 PM
> To: Mukatira, Suraj
> Cc: emboss at emboss.open-bio.org
> Subject: RE: [EMBOSS] EMBOSS EXPLORER installation help. .
> 
> Where there any errors from the install script you ran?  
> 
> Are you able to see your main page?  
> http://<servername>/cgi-bin/emboss?
> 
> 
> 
> > -----Original Message-----
> > From: emboss-bounces at lists.open-bio.org
> > [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of 
> > Mukatira, Suraj
> > Sent: Monday, September 18, 2006 3:54 PM
> > To: emboss at emboss.open-bio.org
> > Subject: [EMBOSS] EMBOSS EXPLORER installation help
> > 
> > 
> > Hi all,
> > I have questions regarding emboss explorer installation.
> > Attached is the explorer configuration file
> > 
> > I have emboss4.0 running in my linux machine: /usr/local/bin
> > and /var/www/emboss
> > 
> > After following instructions on the emboss explorer
> > installation I cannot see the webpage: Not Found The 
> > requested URL /cgi-bin/emboss/intro was not found on this server.
> > 
> > Not Found
> > The requested URL /cgi-bin/emboss/menu was not found on this server
> > 
> > Here are some directory structures:
> > 
> > drwxrwxr-x  2 mukatira mukatira   4096 2006-09-15 14:02 cgi-bin
> > drwxr-xr-x  6 mukatira mukatira   4096 2006-09-18 13:58 emboss
> > drwxrwxr-x  3 mukatira mukatira   4096 2006-09-15 14:02 html
> > -rw-r--r--  1 mukatira mukatira   1457 2006-09-11 14:28 index.html
> > $>:/var/www$ pwd
> > /var/www
> > 
> > Under cgi-bin I do not see a folder 'emboss'
> > 
> > $>/var/www/cgi-bin$ ls -l
> > -rwxrwxr-x 1 root root 110 2006-09-18 14:34 emboss
> > $>:/var/www/cgi-bin$ more emboss #!/usr/bin/perl
> > 
> > use strict;
> > use warnings;
> > 
> > use EMBOSS::GUI;
> > 
> > my $emboss = EMBOSS::GUI->new();
> > $emboss->go();
> > 
> > 
> > 
> > 
> > Thanks in anticipation.
> > Also, what is the best way to completely uninstall emboss.
> > 
> 
> 



From pmr at ebi.ac.uk  Tue Sep 19 12:39:09 2006
From: pmr at ebi.ac.uk (pmr at ebi.ac.uk)
Date: Tue, 19 Sep 2006 13:39:09 +0100 (BST)
Subject: [EMBOSS] [Fwd: RE:  EMBOSS-Explorer Follow-up]
Message-ID: <1622.193.175.249.183.1158669549.squirrel@webmail.ebi.ac.uk>

Hi Ryan,

>> Aha ... tfm works, but tfm -html may fail.
>>
>> If the program fails to find the html file, it will check the
>> original
>> distribution directory. Unfortunately, if it does find an
>> html file ...
>> it may be from version 3. I forgot about the tfm -html option when we
moved the files.
>>
>> A fix will take a few days to test. EMBASSY html documentation is not
under the embassy package, so TFM will have to check the ACD file to
find the EMBASSY package name. Easy enough - several other
>> programs do
>> it - but needs quite a few tests to make sure it does it correctly in
all cases.

I have posted a fix (Fix 18, emboss/tfm.c and nucleus/emboss.[ch]) on the
FTP server ftp://emboss.open-bio.org/pub/EMBOSS/fixes

More information in the README.fixes file.

Apologies for this bug ... I completely forgot there was a -html option in
tfm ... but at least we now have a use for it :-)

regards.

Peter





From mthon at tamu.edu  Tue Sep 19 14:27:44 2006
From: mthon at tamu.edu (Michael Thon)
Date: Tue, 19 Sep 2006 09:27:44 -0500
Subject: [EMBOSS] showfeat: joining compound features
Message-ID: <D9F13423-1AF1-4863-A6FD-EFA254B7F913@tamu.edu>

Hello everyone - I am using showfeat to display blast similarity  
features that are stored in a gff file.  From the documentation, it  
looks like showfeat can display multiple exon features on the same  
line but can it also do this with similarity features?  Here is an  
example from my gff file:

Chr5:4535154,4542653    BLAST   similarity      2475     
5120    .       .       .       Target "ref|XP_468448.1|"
Chr5:4535154,4542653    BLAST   similarity      3142    3480     
388     +       .       Target "ref|XP_468448.1|" 141 225
Chr5:4535154,4542653    BLAST   similarity      4944    5120     
304     +       .       Target "ref|XP_468448.1|" 248 306
Chr5:4535154,4542653    BLAST   similarity      2475    2603     
216     +       .       Target "ref|XP_468448.1|" 66 108
Chr5:4535154,4542653    BLAST   similarity      2916    3017     
182     +       .       Target "ref|XP_468448.1|" 107 140

Also, is there an emboss program that does showfeat's functions but  
with a graphical, publication quality output?  I am thinking of a  
graphic with colored feature tracks, etc.
Thanks
Mike




From thomas.girke at ucr.edu  Tue Sep 19 15:08:44 2006
From: thomas.girke at ucr.edu (Thomas Girke)
Date: Tue, 19 Sep 2006 08:08:44 -0700
Subject: [EMBOSS] showfeat: joining compound features
In-Reply-To: <D9F13423-1AF1-4863-A6FD-EFA254B7F913@tamu.edu>
References: <D9F13423-1AF1-4863-A6FD-EFA254B7F913@tamu.edu>
Message-ID: <20060919150844.GA21474@bioinfo.ucr.edu>

Micheal,

If you know R a little bit then you may want to try this R script. 
http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/featureMap.txt

I often use this script for plotting position information of all kinds of EMBOSS
programs onto genes and chromosomes.

To demo the utility of the script, simply paste this command into the R console:
source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/featureMap.txt")

Best,
Thomas

On Tue 09/19/06 09:27, Michael Thon wrote:
> Hello everyone - I am using showfeat to display blast similarity  
> features that are stored in a gff file.  From the documentation, it  
> looks like showfeat can display multiple exon features on the same  
> line but can it also do this with similarity features?  Here is an  
> example from my gff file:
> 
> Chr5:4535154,4542653    BLAST   similarity      2475     
> 5120    .       .       .       Target "ref|XP_468448.1|"
> Chr5:4535154,4542653    BLAST   similarity      3142    3480     
> 388     +       .       Target "ref|XP_468448.1|" 141 225
> Chr5:4535154,4542653    BLAST   similarity      4944    5120     
> 304     +       .       Target "ref|XP_468448.1|" 248 306
> Chr5:4535154,4542653    BLAST   similarity      2475    2603     
> 216     +       .       Target "ref|XP_468448.1|" 66 108
> Chr5:4535154,4542653    BLAST   similarity      2916    3017     
> 182     +       .       Target "ref|XP_468448.1|" 107 140
> 
> Also, is there an emboss program that does showfeat's functions but  
> with a graphical, publication quality output?  I am thinking of a  
> graphic with colored feature tracks, etc.
> Thanks
> Mike
> 
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
> 

-- 
Thomas Girke, Ph.D.
1008 Noel T. Keen Hall
Center for Plant Cell Biology (CEPCEB)
University of California
Riverside, CA 92521

E-mail: thomas.girke at ucr.edu
Website: http://faculty.ucr.edu/~tgirke
Ph: 951-827-2469
Fax: 951-827-4437


From mthon at tamu.edu  Thu Sep 21 14:04:02 2006
From: mthon at tamu.edu (Michael Thon)
Date: Thu, 21 Sep 2006 09:04:02 -0500
Subject: [EMBOSS] showfeat: joining compound features
In-Reply-To: <20060919150844.GA21474@bioinfo.ucr.edu>
References: <D9F13423-1AF1-4863-A6FD-EFA254B7F913@tamu.edu>
	<20060919150844.GA21474@bioinfo.ucr.edu>
Message-ID: <C4446B21-D1BA-487E-BF96-CC58EC685409@tamu.edu>

Hi Thomas - Thanks for the script, I'm going to try it out.  My need  
the other day was for an easy way to display features that I could  
show to my class.  Showfeat ended up working alright so that's what  
we're using at the moment.  gff2ps is also good at making graphics  
but I thought there should be an emboss way to do it too.
cheers
Mike

On Sep 19, 2006, at 10:08 AM, Thomas Girke wrote:

> Micheal,
>
> If you know R a little bit then you may want to try this R script.
> http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/ 
> featureMap.txt
>
> I often use this script for plotting position information of all  
> kinds of EMBOSS
> programs onto genes and chromosomes.
>
> To demo the utility of the script, simply paste this command into  
> the R console:
> source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/ 
> My_R_Scripts/featureMap.txt")
>
> Best,
> Thomas
>
> On Tue 09/19/06 09:27, Michael Thon wrote:
>> Hello everyone - I am using showfeat to display blast similarity
>> features that are stored in a gff file.  From the documentation, it
>> looks like showfeat can display multiple exon features on the same
>> line but can it also do this with similarity features?  Here is an
>> example from my gff file:
>>
>> Chr5:4535154,4542653    BLAST   similarity      2475
>> 5120    .       .       .       Target "ref|XP_468448.1|"
>> Chr5:4535154,4542653    BLAST   similarity      3142    3480
>> 388     +       .       Target "ref|XP_468448.1|" 141 225
>> Chr5:4535154,4542653    BLAST   similarity      4944    5120
>> 304     +       .       Target "ref|XP_468448.1|" 248 306
>> Chr5:4535154,4542653    BLAST   similarity      2475    2603
>> 216     +       .       Target "ref|XP_468448.1|" 66 108
>> Chr5:4535154,4542653    BLAST   similarity      2916    3017
>> 182     +       .       Target "ref|XP_468448.1|" 107 140
>>
>> Also, is there an emboss program that does showfeat's functions but
>> with a graphical, publication quality output?  I am thinking of a
>> graphic with colored feature tracks, etc.
>> Thanks
>> Mike
>>
>>
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>
> -- 
> Thomas Girke, Ph.D.
> 1008 Noel T. Keen Hall
> Center for Plant Cell Biology (CEPCEB)
> University of California
> Riverside, CA 92521
>
> E-mail: thomas.girke at ucr.edu
> Website: http://faculty.ucr.edu/~tgirke
> Ph: 951-827-2469
> Fax: 951-827-4437



From David.Bauer at SCHERING.DE  Thu Sep 21 07:39:47 2006
From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE)
Date: Thu, 21 Sep 2006 09:39:47 +0200
Subject: [EMBOSS] showfeat: joining compound features
In-Reply-To: <20060919150844.GA21474@bioinfo.ucr.edu>
Message-ID: <OF3D51E382.B49D26C3-ONC12571F0.0029A814-C12571F0.002A1834@schering.de>


Hi,

if your data are in gff format you could also try gff2ps:
http://www1.imim.es/software/gfftools/GFF2PS.html
Within EMBOSS there is also an application lindna but it has its own input
format so you must first convert your gff file to lindna input.

HTH,
David.

emboss-bounces at lists.open-bio.org schrieb am 19/09/2006 17:08:44:

> Micheal,
>
> If you know R a little bit then you may want to try this R script.
>
http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/featureMap.txt

>
> I often use this script for plotting position information of all
> kinds of EMBOSS
> programs onto genes and chromosomes.
>
> To demo the utility of the script, simply paste this command into
> the R console:
> source("http://faculty.ucr.
> edu/~tgirke/Documents/R_BioCond/My_R_Scripts/featureMap.txt")
>
> Best,
> Thomas
>
> On Tue 09/19/06 09:27, Michael Thon wrote:
> > Hello everyone - I am using showfeat to display blast similarity
> > features that are stored in a gff file.  From the documentation, it
> > looks like showfeat can display multiple exon features on the same
> > line but can it also do this with similarity features?  Here is an
> > example from my gff file:
> >
> > Chr5:4535154,4542653    BLAST   similarity      2475
> > 5120    .       .       .       Target "ref|XP_468448.1|"
> > Chr5:4535154,4542653    BLAST   similarity      3142    3480
> > 388     +       .       Target "ref|XP_468448.1|" 141 225
> > Chr5:4535154,4542653    BLAST   similarity      4944    5120
> > 304     +       .       Target "ref|XP_468448.1|" 248 306
> > Chr5:4535154,4542653    BLAST   similarity      2475    2603
> > 216     +       .       Target "ref|XP_468448.1|" 66 108
> > Chr5:4535154,4542653    BLAST   similarity      2916    3017
> > 182     +       .       Target "ref|XP_468448.1|" 107 140
> >
> > Also, is there an emboss program that does showfeat's functions but
> > with a graphical, publication quality output?  I am thinking of a
> > graphic with colored feature tracks, etc.
> > Thanks
> > Mike
> >
> >
> > _______________________________________________
> > EMBOSS mailing list
> > EMBOSS at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/emboss
> >
>
> --
> Thomas Girke, Ph.D.
> 1008 Noel T. Keen Hall
> Center for Plant Cell Biology (CEPCEB)
> University of California
> Riverside, CA 92521
>
> E-mail: thomas.girke at ucr.edu
> Website: http://faculty.ucr.edu/~tgirke
> Ph: 951-827-2469
> Fax: 951-827-4437
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss



From tjc at sanger.ac.uk  Mon Sep 25 13:07:53 2006
From: tjc at sanger.ac.uk (Tim Carver)
Date: Mon, 25 Sep 2006 14:07:53 +0100
Subject: [EMBOSS] Problem Installing Jemboss
In-Reply-To: <be9b52410609180922j602e1f40le2aa0444ff20fa5@mail.gmail.com>
Message-ID: <C13D9339.1CDA6%tjc@sanger.ac.uk>

Hi

For EMBOSS you need zlib, libgd and libpng all in one place and this is what
the script checks for. So you may need to ensure that is the case and if
necessary use the  --with-pngdriver (on option when you run the install
script) flag to define where.

Regards
Tim Carver


On 18/9/06 17:22, "Abhishek Pratap" <abhishek.vit at gmail.com> wrote:

> I am unable to install jemboss on solaris 10. with all the dependencies
> installed (png, gd etc) i am getting this error.
> 
> 
> This is the error i get each
> 
> ------------------------- WARNING ----------------------------
> 
> The script has detected that /usr/include/gd.h
> does not exist
> 
> Download gd from
>        http://www.boutell.com/gd/
> 
> For details see the EMBOSS admin guide:
> http://emboss.sourceforge.net/admin/
> 
> To exit use Control C or press return to continue.
> 
> --------------------------------------------------------------
> 
> 
> 
>>>>>> 
> the gd.h file is allready present in the /usr/include
> 
> Can someone guide me  on this




From sea99.wang at gmail.com  Mon Sep 25 16:30:57 2006
From: sea99.wang at gmail.com (Sea)
Date: Tue, 26 Sep 2006 00:30:57 +0800
Subject: [EMBOSS] EMBOSS Explorer "bad substitution"
Message-ID: <4f3a50530609250930x3c68292h32eda9207fb5124f@mail.gmail.com>

Hello Everybody,

I met another problem....
When I ran "install" of emboss explorer
and it started to do the job,
but I always got this message "bad substitution" and then quit.
Could any expenience friends provide me a solution?
Thanks a lot!

Here is the logs:


# ./install
installing EMBOSS Explorer perl modules...

'PREREQ_FATAL' is not a known MakeMaker parameter name.
Writing Makefile for EMBOSS::GUI
Manifying blib/man3/EMBOSS::GUI.3
Manifying blib/man3/EMBOSS::GUI::XHTML.3
Manifying blib/man3/EMBOSS::GUI::Conf.3
Manifying blib/man3/EMBOSS::ACD.3
Manifying blib/man3/EMBOSS::GUI.3
Installing /usr/perl5/site_perl/5.6.1/EMBOSS/GUI.pm
Installing /usr/perl5/site_perl/5.6.1/EMBOSS/ACD.pm
Installing /usr/perl5/site_perl/5.6.1/EMBOSS/GUI/XHTML.pm
Installing /usr/perl5/site_perl/5.6.1/EMBOSS/GUI/Conf.pm
Installing /usr/perl5/5.6.1/man/man3/EMBOSS::GUI.3
Installing /usr/perl5/5.6.1/man/man3/EMBOSS::GUI::XHTML.3
Installing /usr/perl5/5.6.1/man/man3/EMBOSS::GUI::Conf.3
Installing /usr/perl5/5.6.1/man/man3/EMBOSS::ACD.3
Writing
/usr/perl5/site_perl/5.6.1/sun4-solaris-64int/auto/EMBOSS/GUI/.packlist
Appending installation info to
/usr/perl5/5.6.1/lib/sun4-solaris-64int/perllocal.pod
`install' is up to date.
installing EMBOSS Explorer GUI components...


I need to collect some information in order to install EMBOSS Explorer:
./install: embossversion: not found
-e Where was EMBOSS installed?
        (default is /usr/local)
/bioserver/emboss/share
-e Where should the EMBOSS Explorer HTML files be installed?
        (default is /var/www/html/emboss)
/bioserver/emboss/share/GUI/htdocs
-e What is the URL prefix corresponding to the HTML directory above?
        (default is /emboss)
 [use default setting]
-e Where should the EMBOSS Explorer CGI script be installed?
        (default is /var/www/cgi-bin/emboss)
/bioserver/emboss/share/GUI/cgi-bin
./install: bad substitution     [<-- always got this....  : ( ]


From tjc at sanger.ac.uk  Tue Sep 26 09:26:28 2006
From: tjc at sanger.ac.uk (Tim Carver)
Date: Tue, 26 Sep 2006 10:26:28 +0100
Subject: [EMBOSS] Jemboss problems with fuzzpro and fuzznuc
In-Reply-To: <4507DB32.7040903@cancer.org.uk>
Message-ID: <C13EB0D4.1D332%tjc@sanger.ac.uk>

Hi Neil

Thanks for your message. This is a known bug. As far as I understand the new
pattern qualifier has associated qualifiers -pmismatch (also pformat and
pname) which Jemboss does not know about (yet) as it just treats the pattern
as a string.

Cheers
Tim

On 13/9/06 11:19, "Neil Brookes" <neil.brookes at cancer.org.uk> wrote:

> Hi,
> 
> I think I have unearthed an issue with fuzzpro/fuzznuz and EMBOSS 4.0.0
> The old version in 3.0.0 had a '-mismatch' option. This has changed in
> version 4.0.0 to '-pmismatch'.
> 
> The 'mismatch' integer element seems to have been removed from the
> fuzzpro/nuc ACD files.
> I'm not sure how/when Jemboss parses the ACD flies, but it doesn't seem
> to be allowing for the  new '-pmismatch' option, and users are unable to
> specify a value.
> 
> any ideas ?
> 
> cheers
> Neil




From gbottu at ben.vub.ac.be  Thu Sep 28 13:57:40 2006
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Thu, 28 Sep 2006 15:57:40 +0200
Subject: [EMBOSS] case sensitive identifiers - Checked by AntiVir DEMO
	version -
Message-ID: <20060928135740.GA14320@bigben.ulb.ac.be>

	Dear colleagues,

Thure Etzold, the developer of SRS, once said "You cannot imagine anything 
that crazy or there is at least one database manager who really does it". 
While trying to put in our MRS server databanks with the protein and 
nucleic acid sequences extracted from the PDB, I bumped on the following 
problem : some have identifiers only different by case. E.g. there is a 
1fnt_A and a 1fnt_a. Now, most bioinformatic software is not case 
sensitive. I understand that MRS stores indices so that they can be 
displayed in their original case, but can only be searched
case-insensitively ; it does automatically modify redundant indices, e.g. 
1fnt_a is stored as 1fnt_a_12835. This is however not ideal. Should MRS 
be adapted so that it can handle case sensitive indices ? This will 
however not solve everything, since other software like EMBOSS or GCG is 
also case insensitive. My idea is to let the MRS parser store 1fnt_aLC
(LC means lowercase) as identifier. A user can then search for the 
sequence he needs in MRS and in EMBOSS (if the EMBOSS installation uses 
MRS as databank access mechanism) ask for the sequence pdbprot:1fnt_alc.
This would of course also work with 1fnt_a_12835 but it avoids the use of 
a meaningless and irreproducible number. Anybody a comment ?

	Regards,
	Guy Bottu,
	Belgian EMBnet Node



From pmr at ebi.ac.uk  Thu Sep 28 14:32:36 2006
From: pmr at ebi.ac.uk (Peter Rice)
Date: Thu, 28 Sep 2006 15:32:36 +0100
Subject: [EMBOSS] [Mrs-user] case sensitive identifiers
In-Reply-To: <20060928135740.GA14320@bigben.ulb.ac.be>
References: <20060928135740.GA14320@bigben.ulb.ac.be>
Message-ID: <451BDD04.9040806@ebi.ac.uk>

Guy Bottu wrote:
> My idea is to let the MRS parser store 1fnt_aLC
> (LC means lowercase) as identifier. A user can then search for the 
> sequence he needs in MRS and in EMBOSS (if the EMBOSS installation uses 
> MRS as databank access mechanism) ask for the sequence pdbprot:1fnt_alc.
> This would of course also work with 1fnt_a_12835 but it avoids the use of 
> a meaningless and irreproducible number. Anybody a comment ?

Not a general solution, but for PDB chains you could use an extra 
underscore for the lower case ones.

For EMBOSS .... well, we could play with the way databases work. Not all 
access methods allow case sensitive searching, but we could fetch all 
entries and try to reject those that do not match. This would need 
something in the EMBOSS id. We already allow modifiers after the id to 
set sequence ranges pdbprot:1fbt_a[1:20] or we could add a qualifier 
-scasesensitive for all sequence inputs.

Peter


From gbottu at ben.vub.ac.be  Fri Sep 29 08:15:08 2006
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Fri, 29 Sep 2006 10:15:08 +0200
Subject: [EMBOSS] case sensitive identifiers - Checked by AntiVir DEMO
	version -
In-Reply-To: <451BDD04.9040806@ebi.ac.uk>
References: <20060928135740.GA14320@bigben.ulb.ac.be>
	<451BDD04.9040806@ebi.ac.uk>
Message-ID: <20060929081508.GA25906@bigben.ulb.ac.be>

On Thu, Sep 28, 2006 at 03:32:36PM +0100, Peter Rice wrote:
> For EMBOSS .... well, we could play with the way databases work. Not all 
> access methods allow case sensitive searching, but we could fetch all 
> entries and try to reject those that do not match. This would need 
> something in the EMBOSS id. We already allow modifiers after the id to 
> set sequence ranges pdbprot:1fbt_a[1:20] or we could add a qualifier 
> -scasesensitive for all sequence inputs.

For the moment our emboss.default contains :

DB pdbprot [ type: P format: fasta comment: 'protein sequences from PDB'
     methodquery: app app: "/nfsben/srs/bin/linux73/getz -e '[pdbprot-id:%s]'"
             methodall: direct dir: /nfsben/srs/data/blast/dbfb/pdb file: pdb
]

and seqret pdbprot:1ml5_s yields :

>1ml5_S 30S RIBOSOMAL PROTEIN S16
MVKIRLARFGSKHNPHYPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLKVDVERAR
YWLSVGAQPTDTARRLLRQAGVFRQEAREGA
>1ml5_s 50S RIBOSOMAL PROTEIN L22
MEAKAIARYVRISPRKVRLVVDLIRGKSLEEARNILRYTNKRGAYFVAKVLESAAANAVN
NHDMLEDRLYVKAAYVDEGPALKRVLPRARGRADIIKKRTSHITVILGEKHGK

So, your idea of fetching all entries and then parsing them would work 
for SRS. I however think that instead of an associated parameter  
-scasesensitive it would be better to have in the emboss.default syntax 
for DB entries an optional parameter case:. You should be able to handle 
the situation where it is appropriate to pass an id to a case sensitive 
search method and the situation where it is appropriate to parse the 
output of a case-insensitive search method. This can best be decided for each 
databank at EMBOSS site configuartion time, rather than at sequence 
retrieval time. What do you think ?

	Regards,
	Guy Bottu



From pmr at ebi.ac.uk  Fri Sep 29 08:28:22 2006
From: pmr at ebi.ac.uk (pmr at ebi.ac.uk)
Date: Fri, 29 Sep 2006 09:28:22 +0100 (BST)
Subject: [EMBOSS] case sensitive identifiers - Checked by AntiVir DEMO
	version -
In-Reply-To: <20060929081508.GA25906@bigben.ulb.ac.be>
References: <20060928135740.GA14320@bigben.ulb.ac.be>
	<451BDD04.9040806@ebi.ac.uk>
	<20060929081508.GA25906@bigben.ulb.ac.be>
Message-ID: <2023.86.132.219.183.1159518502.squirrel@webmail.ebi.ac.uk>

Dear Guy,

> So, your idea of fetching all entries and then parsing them would work
> for SRS. I however think that instead of an associated parameter
> -scasesensitive it would be better to have in the emboss.default syntax
> for DB entries an optional parameter case:. You should be able to handle
> the situation where it is appropriate to pass an id to a case sensitive
> search method and the situation where it is appropriate to parse the
> output of a case-insensitive search method. This can best be decided for
> each
> databank at EMBOSS site configuartion time, rather than at sequence
> retrieval time. What do you think ?

You are right. Excellent idea. I will do it ASAP.

It will mean a new attribute stored for sequence database access.

For the PDB case, really only the end of the ID is case-sensitive. Do you
think the database should be case-sensitive for the whole ID, or does it
make sense to check for a pattern as the case-sensitive part?

EMBOSS will initially read only one sequence for a seqall ... it does not
read in all the sequences and look for duplicates so we have to decide in
the emboss.defaults DB definition how to check a single ID (no way to read
them all and check for duplicates).

regardrs,

Peter




From pmr at ebi.ac.uk  Fri Sep 29 10:27:51 2006
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 29 Sep 2006 11:27:51 +0100
Subject: [EMBOSS] case sensitive identifiers
In-Reply-To: <20060929081508.GA25906@bigben.ulb.ac.be>
References: <20060928135740.GA14320@bigben.ulb.ac.be>
	<451BDD04.9040806@ebi.ac.uk>
	<20060929081508.GA25906@bigben.ulb.ac.be>
Message-ID: <451CF527.8040506@ebi.ac.uk>

Guy Bottu wrote:
> For the moment our emboss.default contains :
> 
> DB pdbprot [ type: P format: fasta comment: 'protein sequences from PDB'
>      methodquery: app app: "/nfsben/srs/bin/linux73/getz -e '[pdbprot-id:%s]'"
>              methodall: direct dir: /nfsben/srs/data/blast/dbfb/pdb file: pdb
> ]

That raises a new problem .... the "app" method will work, but "srs" and 
"srswww" will not.

They search for a pdbprot-acc match and there is no acc field.

I will add a new database attribute hasaccession (default "Y") so 
searches know whether the acc field can be used. Unfortunately the 
fields attribute is defined as "everything except id and acc" so I 
cannot use it.

So, there will be 2 new (and for the first time boolean) attributes for 
databases. To use them, you will need:

caseidmatch: "Y"
hasaccession: "N"

These will also be the first to use the default values for database 
attributes! All other default values are empty strings :-)

regards,

Peter