From tmargus at ebc.ee  Sun Mar 13 11:34:12 2005
From: tmargus at ebc.ee (=?ISO-8859-4?Q?T=F5nu_Margus?=)
Date: Sun, 13 Mar 2005 18:34:12 +0200
Subject: [EMBOSS] problems with indexing RDP SSU_RNA  aligned version with dbflat and dbifasta
Message-ID: <20050313162328.A7B6751927@mercury.hgmp.mrc.ac.uk>

Hi, 

 

I fall in to problems when I tried to index alignes SSU_RRNA sequences from
RDP release 9.26  (both fasta and GB format).

Both files are large than 2 GB (fasta is 5GB and is ca 7GB). 

 

It seems to me that dbflat and dbfasta  (EMBOSS rel 2.9) cannot manage with
wiles what are large than 2 GB in my Mandrake Linux 9.2.

 

If this is correct what could be solution?

 

Is it possible to let them index files form stdin?    Someting like   cat
release_9.26_aligned.fasta    | dbfasta   -bla  -bla -blaa  

  

or  must I split it in to  smaller parts than  2GB?

 

If the spliting is only way is there some tool what can do it correctly for
genbanck format?

 

 

 

Thanks in advance

 

T?nu Margus

 

 

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From fernan at iib.unsam.edu.ar  Tue Mar 15 12:36:39 2005
From: fernan at iib.unsam.edu.ar (Fernan Aguero)
Date: Tue, 15 Mar 2005 14:36:39 -0300
Subject: [EMBOSS] EMBOSS 2.10.0 released
In-Reply-To: <200502200004.j1K04J2l014579@bromine.hgmp.mrc.ac.uk>
References: <200502200004.j1K04J2l014579@bromine.hgmp.mrc.ac.uk>
Message-ID: <20050315173639.GC80393@iib.unsam.edu.ar>

+----[ Alan Bleasby <ableasby at hgmp.mrc.ac.uk> (19.Feb.2005 21:09):
|
| EMBOSS 2.10.0 can be downloaded from the following URL:
| 
|    ftp://ftp.rfcgr.mrc.ac.uk/pub/EMBOSS/
| 
| or via the EMBOSS homepage:
| 
|    http://emboss.sourceforge.net
|
+----]

Alan,

I'm now updating the FreeBSD ports to 2.10.0, and noticed
that the new MYEMBOSS-1.0.0.tar.gz can't be found in the
main site nor in any mirror.

Should I wait and include this on the list of embassy
apps? Also, when will be avilable the PHILIPNEW embassy
package?

While we're here, a few minor issues:
i) on the emboss.sf.net main page the latest release is still 2.9.0
ii) what are the requirements for OSs to enter the 'It is
reported to work' category on the 'System requirements'
section of the /download/ page? Maybe FreeBSD can be moved
to this category?

Thanks for the good work,

Fernan


From ableasby at hgmp.mrc.ac.uk  Tue Mar 15 16:58:18 2005
From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby)
Date: Tue, 15 Mar 2005 21:58:18 GMT
Subject: [EMBOSS] EMBOSS 2.10.0 released
Message-ID: <200503152158.j2FLwIg0002323@bromine.hgmp.mrc.ac.uk>

Thanks for the feedback Fernan.
FreeBSD had to slip down the list when your predecessor was
no longer able to do the port (although we did make sure that
EMBOSS compiled on that OS ... it just wasn't packaged in
the FreeBSD style). Thanks for taking that over. We'll adjust
the web pages.

PHYLIPNEW and MYEMBOSS are still undergoing testing. We will be
updating phylipnew before its release. We'd hope to get it
out by July. Myemboss is a developers package rather than an
application so it doesn't need to be provided in any standard
release. However, by July for that too.

Cheers
Alan


From stefanielager at fastmail.ca  Tue Mar 22 08:20:07 2005
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Tue, 22 Mar 2005 13:20:07 +0000 (UTC)
Subject: [EMBOSS] Including exonerate in EMBOSS?
Message-ID: <20050322132008.291CE8613B0@mail.interchange.ca>

Hi,

Has anyone considered including the exonerate alignment algorithm
(Slater & Birney 2005) into EMBOSS? Exonerate could replace most of the
alignment algorithms currently available in EMBOSS, and it's much
faster. Exonerate would probably also benefit, by addition of yet more
output options and integration with current EMBOSS applications.    

Stefanie


Slater GS, Birney E. 
Automated generation of heuristics for biological sequence comparison.
BMC Bioinformatics. 2005 Feb 15;6(1):31.
_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians



From pmr at ebi.ac.uk  Wed Mar 30 10:50:10 2005
From: pmr at ebi.ac.uk (Peter Rice)
Date: Wed, 30 Mar 2005 16:50:10 +0100
Subject: [EMBOSS] Codon usage file improvements
Message-ID: <424ACAB2.8090509@ebi.ac.uk>

A quick check before I make changes to the EMBOSS codon usage files.

EMBOSS includes a set of codon usage files in the emboss/data/CODONS directory 
which are installed for use. The cutgextract program allows administrators to 
install codon usage tables for all species using the cutg database.

The files provided with EMBOSS were from Mike Cherry's 1992 "codonusage" 
database and from a 1994 release of the "transterm" database.

The file names are usually in the format "Egss" where "g" is the first letter 
of the genus, and "ss" is the first 2 letters of the species. Like SwissProt, 
there are a few exceptions (Eyeast for example). The filenames came from these 
databases originally - they were not made up by them EMBOSS team (we only 
added the "E" at the start).

I am modifying cutgextract to include more information in the output files, 
and will update the files in this directory where possible, using data from 
the latest cutg.

Are there any files in emboss/data/CODONS that are particular favourites and 
need to be preserved?

Are there any non-standard .cut filenames in emboss/data/CODONS that will 
cause problems if they are removed?

(Administrators will need to remove the old filenames by hand when they 
install a new version of EMBOSS - we cannot easily remove them automatically).

I will also allow a choice of codon usage file formats - are there any special 
formats that are useful for exchange with other packages?

regards,

Peter Rice




From robin at hms.harvard.edu  Wed Mar 30 11:47:12 2005
From: robin at hms.harvard.edu (Robin Colgrove)
Date: Wed, 30 Mar 2005 11:47:12 -0500
Subject: [EMBOSS] OS X install fails with "ld: can't locate file for: -lX11"
Message-ID: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu>


Hello all,

I am new to the list. Apologies if this is an FAQ. I could not find it 
in the archives.
Anyway, I am running OS X 10.3.8 and downloaded the latest EMBOSS, 
2.10.0.
I followed the instruction for installation, ./configure, then
sudo make
which goes on for a long time, compiling an lot of things, but then 
finally fails with:
[...lots of stuff compiled OK...]
source='aaindexextract.c' object='aaindexextract.o' libtool=no \
DEPDIR=.deps depmode=gcc /bin/sh ../depcomp \
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" 
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" 
-DVERSION=\"2.10.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DX_DISPLAY_MISSING=1 
-DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 
-DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 
-DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 
-DHAVE_MEMMOVE=1 -DHAVE_LIBM=1  -I. -I. -I../nucleus -I../ajax 
-I../plplot  -DAJ_MACOSXLF  -DBENDIAN -DNO_AUTH  -O2 -c 
aaindexextract.c
/bin/sh ../libtool --tag=CC --mode=link gcc  -O2   -o aaindexextract  
aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la 
../ajax/libajax.la ../plplot/libplplot.la -lX11  -lm
mkdir .libs
gcc -O2 -o .libs/aaindexextract aaindexextract.o  
../nucleus/.libs/libnucleus.dylib ../ajax/.libs/libajaxg.dylib 
../ajax/.libs/libajax.dylib ../plplot/.libs/libplplot.dylib -lX11 -lm
ld: can't locate file for: -lX11
make[2]: *** [aaindexextract] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

[...and then exits...]

just to see if it would work, I tried
sudo make install
which installed a lot of things but then failed with:

/bin/sh ../libtool --tag=CC --mode=link gcc  -O2   -o aaindexextract  
aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la 
../ajax/libajax.la ../plplot/libplplot.la -lX11  -lm
gcc -O2 -o .libs/aaindexextract aaindexextract.o  
../nucleus/.libs/libnucleus.dylib ../ajax/.libs/libajaxg.dylib 
../ajax/.libs/libajax.dylib ../plplot/.libs/libplplot.dylib -lX11 -lm
ld: can't locate file for: -lX11
make[2]: *** [aaindexextract] Error 1
make[1]: *** [install-recursive] Error 1
make: *** [install-recursive] Error 1

Hoping it would work anyway, I tried the tutorial and the first example:
%wossname
fails with
tcsh: wossname: Command not found.
even though I see:
/usr/local/share/EMBOSS/acd/wossname.acd

My knowledge of these things is rudimentary, but the error seems to be 
complaining about not finding X11, but that can't be right, since I 
have
X11 1.0 - XFree86 4.3.0
and have been using it for other programs like Phred/Phrap/Consed.

Does anyone know what this error means and how to fix it?

thanks

robin colgrove
department of microbiology
harvard medical school



From andrespinzon at gmail.com  Wed Mar 30 12:22:20 2005
From: andrespinzon at gmail.com (Andres Pinzon)
Date: Wed, 30 Mar 2005 12:22:20 -0500
Subject: [EMBOSS] OS X install fails with "ld: can't locate file for: -lX11"
In-Reply-To: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu>
References: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu>
Message-ID: <8968fc7e05033009225e9aabd4@mail.gmail.com>

On Wed, 30 Mar 2005 11:47:12 -0500, Robin Colgrove
<robin at hms.harvard.edu> wrote:

> My knowledge of these things is rudimentary, but the error seems to be
> complaining about not finding X11, but that can't be right, since I
> have
> X11 1.0 - XFree86 4.3.0
> and have been using it for other programs like Phred/Phrap/Consed.
> 
> Does anyone know what this error means and how to fix it?

Sure, all you have to do is to install the development (devel)
libraries for xfree86, (something like Xfree86-4.3.9-devel.....), some
systems doesnt install this libraries by default, since are not
commonly used, some others dont even provide them (red hat, for
instance).
In fact you have 2 possibilities, the first one is to install the
development packages for your Xfree86 version (as ialready commented),
the other one is to install EMBOSS without X support:
                      ./configure --without-x

With this option you wont have problems with the X stystem but EMBOS
will not be able to plot imges in the X windows system (used by
plotorf, for example).

This is the command i run once i installed the devel packages:

   ./configure --with-pngdriver=/usr/lib/ --prefix=/usr/local/emboss

Ok, i hope this will help you.
-- 
---------
Andr?s Pinz?n [http://www.andrespinzon.com]   
Centro de Bioinformatica, Instituto de Biotecnologia
http://bioinf.ibun.unal.edu.co
Universidad Nacional de Colombia
tel. 3165000 ext. 16961   
GNU/Linux ...para un mundo libre!
----------


From gbottu at ben.vub.ac.be  Wed Mar 30 12:21:18 2005
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Wed, 30 Mar 2005 19:21:18 +0200
Subject: [EMBOSS] CODON USAGE TABLES
Message-ID: <20050330172118.GA14064@bigben.ulb.ac.be>

	Dear Peter, dear all,

A few thoughts on the codon usage tables, now that you are working on 
them.

Do you intend to drop the existing tables from the distribution in favor 
of tables from CUTG ? CUTG has one drawback : the entries for each 
organism/organelle are made from all the genes, without taking account of 
the fact that there exist distinct subpopulations. E.g. in E. coli there 
are the highly expressed genes, the lowly expressed genes and the 
horizontally transferred genes, which have different codon usage. I think 
that in the distribution there are at least for some organisms specific 
files (e.g. Eeco.cut and Eeco_h.cut). The great problem with the files 
from the current distribution is that it is hard to find out which file 
contains what.

There is the issue of the number of files in the face of GUI's. Some GUI's 
for EMBOSS generate a selector from which the user can choose a codon 
usage table. If the complete CUTG has been extracted and installed, this 
does not work well anymore. A selector with more than 10000 entries is not 
convenient and furthermore, in a WWW interface the HTML page takes a 
perceptibly long time to download.
At the BEN site I solved this the following (not necessarily satisfactory) 
way : I modified cutgextract so that it creates files with extension .cutg 
rather than .cut. The interface wEMBOSS only shows the *.cut files in the 
selector. If a user wants to use a CUTG rather than a standard 
distribution file under wEMBOSS, he must first copy it to his project 
using embossdata (at the command line there is no problem).

As formats, it would of course be nice if EMBOSS programs could read and 
write codon usage tables (and other data) in any format, just as they do 
for sequences. Which formats should we support besides what EMBOSS uses 
now ? Is there such a thing as "native" CUTG format (with one entry a 
file) ?. I know about GCG format (not useful for us, but other people 
certainly might want it). There is Staden format. Staden format supports 
also files with 2 tables (codon usage in genes + trinucleotide frequency 
in noncoding DNA) ; what to do with this ? only read the first ? There is 
also the format used by CODEHOP 
(http://blocks.fhcrc.org/blocks/codehop.html). Does 
someone know other formats ?

	Regards,
	Guy Bottu,
	Belgian EMBnet Node
 


From robin at hms.harvard.edu  Wed Mar 30 21:23:21 2005
From: robin at hms.harvard.edu (Robin Colgrove)
Date: Wed, 30 Mar 2005 21:23:21 -0500
Subject: [EMBOSS] More on EMBOSS install on OS X: refuses to overwrite X11
In-Reply-To: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu>
References: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu>
Message-ID: <b149de611d71cdea5b437885845aa87a@hms.harvard.edu>


Many thanks to all who suggested fixes for an OS X emboss install.
Not having time to mix and match, I tried them all. After a few failed  
attempts to try them one by one.

I updated to the latest X11SDK in the Xcode1.5 package.
I updated fink to the latest 0.71 version.
and then I tried using fink to install emboss.

It went on for a couple of _hours_, installing a huge number of things  
but then finally dumped me out, complaining that there is an existing  
X11 distribution and telling me to remove it. This is sort of  
obnoxious, since I use my existing X11 for sequence assembly with  
consed, and it works fine and is important to my work. Fink/emboss  
gives me no assurance that it will not screw up what I have working  
already (and which took me no small amount of effort to get working),  
so I am not about to blithely remove my existing X11 without some way  
to know that I will not mess up what is working now.

I thought maybe everything _but_ X11 got installed, but even the first  
example in the tutorial fails:
[dhc017077:~] robin% wossname
tcsh: wossname: Command not found.
[dhc017077:~] robin% man wossname
No manual entry for wossname

So now I cannot tell whether anything at all is working or what to do  
to debug it. Fink seems to have downloaded, compiled and installed  
hundreds of files on my machine but not given me any working programs.  
Very frustrating.

below are the last few lines of installer output.
Any advice on where to go from here appreciated...

robin

************

dpkg-deb: building package `xfree86-shlibs' in  
`/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/xfree86- 
shlibs_4.4.0-13_darwin-powerpc.deb'.
dpkg -i  
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/ 
xfree86_4.4.0-13_darwin-powerpc.deb  
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/xfree86- 
shlibs_4.4.0-13_darwin-powerpc.deb
Selecting previously deselected package xfree86.
(Reading database ... 4015 files and directories currently installed.)
Unpacking xfree86 (from .../xfree86_4.4.0-13_darwin-powerpc.deb) ...
WARNING: if you compile X11 applications against this XFree86 release,
you will *not* be able to run them if you decide to revert to Apple's
X11 provided with Panther.

You have an existing X11 installation in /usr/X11R6 and/or /etc/X11.
This package refuses to overwrite these. Remove them, then tell Fink to
install xfree86 again. (The package won't be recompiled.) If you want
to keep your X11 installation, install system-xfree86 resp.  
system-xtools
instead to make this known to Fink's package system.

Press Return to continue.

dpkg: error processing  
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/ 
xfree86_4.4.0-13_darwin-powerpc.deb (--install):
  subprocess pre-installation script returned error exit status 1
Selecting previously deselected package xfree86-shlibs.
Unpacking xfree86-shlibs (from  
.../xfree86-shlibs_4.4.0-13_darwin-powerpc.deb) ...

You have an existing X11 installation in /usr/X11R6/lib.
This package refuses to overwrite these. Remove them, then tell Fink to
install xfree86-shlibs again. (The package won't be recompiled.)

Press Return to continue.

dpkg: error processing  
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/xfree86- 
shlibs_4.4.0-13_darwin-powerpc.deb (--install):
  subprocess pre-installation script returned error exit status 1
Errors were encountered while processing:
   
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/ 
xfree86_4.4.0-13_darwin-powerpc.deb
   
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/xfree86- 
shlibs_4.4.0-13_darwin-powerpc.deb
### execution of dpkg failed, exit code 1
Failed: can't batch-install packages:  
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/ 
xfree86_4.4.0-13_darwin-powerpc.deb  
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/xfree86- 
shlibs_4.4.0-13_darwin-powerpc.deb


On Mar 30, 2005, at 11:47 AM, Robin Colgrove wrote:

>
> Hello all,
>
> I am new to the list. Apologies if this is an FAQ. I could not find it  
> in the archives.
> Anyway, I am running OS X 10.3.8 and downloaded the latest EMBOSS,  
> 2.10.0.
> I followed the instruction for installation, ./configure, then
> sudo make
> which goes on for a long time, compiling an lot of things, but then  
> finally fails with:
> [...lots of stuff compiled OK...]
> source='aaindexextract.c' object='aaindexextract.o' libtool=no \
> DEPDIR=.deps depmode=gcc /bin/sh ../depcomp \
> gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"  
> -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\"  
> -DVERSION=\"2.10.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1  
> -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1  
> -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1  
> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DX_DISPLAY_MISSING=1  
> -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1  
> -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1  
> -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1  
> -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1  -I. -I. -I../nucleus -I../ajax  
> -I../plplot  -DAJ_MACOSXLF  -DBENDIAN -DNO_AUTH  -O2 -c  
> aaindexextract.c
> /bin/sh ../libtool --tag=CC --mode=link gcc  -O2   -o aaindexextract   
> aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la  
> ../ajax/libajax.la ../plplot/libplplot.la -lX11  -lm
> mkdir .libs
> gcc -O2 -o .libs/aaindexextract aaindexextract.o   
> ../nucleus/.libs/libnucleus.dylib ../ajax/.libs/libajaxg.dylib  
> ../ajax/.libs/libajax.dylib ../plplot/.libs/libplplot.dylib -lX11 -lm
> ld: can't locate file for: -lX11
> make[2]: *** [aaindexextract] Error 1
> make[1]: *** [all-recursive] Error 1
> make: *** [all-recursive] Error 1
>
> [...and then exits...]
>
> just to see if it would work, I tried
> sudo make install
> which installed a lot of things but then failed with:
>
> /bin/sh ../libtool --tag=CC --mode=link gcc  -O2   -o aaindexextract   
> aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la  
> ../ajax/libajax.la ../plplot/libplplot.la -lX11  -lm
> gcc -O2 -o .libs/aaindexextract aaindexextract.o   
> ../nucleus/.libs/libnucleus.dylib ../ajax/.libs/libajaxg.dylib  
> ../ajax/.libs/libajax.dylib ../plplot/.libs/libplplot.dylib -lX11 -lm
> ld: can't locate file for: -lX11
> make[2]: *** [aaindexextract] Error 1
> make[1]: *** [install-recursive] Error 1
> make: *** [install-recursive] Error 1
>
> Hoping it would work anyway, I tried the tutorial and the first  
> example:
> %wossname
> fails with
> tcsh: wossname: Command not found.
> even though I see:
> /usr/local/share/EMBOSS/acd/wossname.acd
>
> My knowledge of these things is rudimentary, but the error seems to be  
> complaining about not finding X11, but that can't be right, since I  
> have
> X11 1.0 - XFree86 4.3.0
> and have been using it for other programs like Phred/Phrap/Consed.
>
> Does anyone know what this error means and how to fix it?
>
> thanks
>
> robin colgrove
> department of microbiology
> harvard medical school
>


From andrespinzon at gmail.com  Wed Mar 30 22:14:35 2005
From: andrespinzon at gmail.com (Andres Pinzon)
Date: Wed, 30 Mar 2005 22:14:35 -0500
Subject: [EMBOSS] More on EMBOSS install on OS X: refuses to overwrite X11
In-Reply-To: <b149de611d71cdea5b437885845aa87a@hms.harvard.edu>
References: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu>
	 <b149de611d71cdea5b437885845aa87a@hms.harvard.edu>
Message-ID: <8968fc7e0503301914488d36b@mail.gmail.com>

On Wed, 30 Mar 2005 21:23:21 -0500, Robin Colgrove
<robin at hms.harvard.edu> wrote:
> 
> Many thanks to all who suggested fixes for an OS X emboss install.
> Not having time to mix and match, I tried them all. After a few failed
> attempts to try them one by one.

Robin, what happened when you tried to configure EMBOSS with the
"--without-x" option? What error did you get?
Did you also tried to install the devel packages?
I had exactly the same problem (in a Linux box) and that was the way i
fixed it. Now my EMBOSS installation runs ok, with wEMBOSS and
EMBOSS::GUI.
-- 
---------
Andr?s Pinz?n [http://www.andrespinzon.com]   
Centro de Bioinformatica, Instituto de Biotecnologia
http://bioinf.ibun.unal.edu.co
Universidad Nacional de Colombia
tel. 3165000 ext. 16961   
GNU/Linux ...para un mundo libre!
----------


From kvddrift at earthlink.net  Thu Mar 31 06:40:59 2005
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Thu, 31 Mar 2005 06:40:59 -0500
Subject: [EMBOSS] More on EMBOSS install on OS X: refuses to overwrite X11
In-Reply-To: <b149de611d71cdea5b437885845aa87a@hms.harvard.edu>
References: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu> <b149de611d71cdea5b437885845aa87a@hms.harvard.edu>
Message-ID: <bd2e28683bc7b81f575e459d83174102@earthlink.net>


On Mar 30, 2005, at 9:23 PM, Robin Colgrove wrote:

> You have an existing X11 installation in /usr/X11R6 and/or /etc/X11.
> This package refuses to overwrite these. Remove them, then tell Fink to
> install xfree86 again. (The package won't be recompiled.) If you want
> to keep your X11 installation, install system-xfree86 resp.  
> system-xtools
> instead to make this known to Fink's package system.
>

Sorry that fink is giving you so much problems. It can indeed be  
frustrating for new users, especially with all the X11 options. If I  
understand it correctly, you are building xfree86 from fink, but you  
already have it installed by yourself. I suggest you remove (or better,  
move it to a temp folder so you can always move it back) the /usr/X11R6  
and /etc/X11 directories, and try the fink package again. You have to  
make sure that you install everyting from the same package, don't mix  
and match your xfree86 with apple's X11, or fink's xorg. See also this  
entry in the fink FAQ:

http://fink.sourceforge.net/faq/usage-general.php?phpLang=en#x-options

> dpkg: error processing  
> /sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/ 
> xfree86_4.4.0-13_darwin-powerpc.deb (--install):

I see that you are using the stable tree from fink. Emboss 2.10 is so  
far only available in the unstable tree. This doesn't mean that it is  
not working, it means that there hasn't been feedback from users that  
it is working with or without problems. Please keep me informed if you  
got it to work, since I am the maintainer of the emboss package in  
fink. If you give me positive feeedback, I can move it to the stable  
tree.

http://fink.sourceforge.net/faq/usage-fink.php?phpLang=en#unstable


Finally, if everything went fine, I can highly recommend the  
emboss-kaptain package from fink which will give you a very nice GUI in  
X11.

good luck,

- Koen.



From robin at hms.harvard.edu  Thu Mar 31 09:46:00 2005
From: robin at hms.harvard.edu (Robin Colgrove)
Date: Thu, 31 Mar 2005 09:46:00 -0500
Subject: [EMBOSS] More on EMBOSS install on OS X: refuses to overwrite X11
In-Reply-To: <bd2e28683bc7b81f575e459d83174102@earthlink.net>
References: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu> <b149de611d71cdea5b437885845aa87a@hms.harvard.edu> <bd2e28683bc7b81f575e459d83174102@earthlink.net>
Message-ID: <d88d25794e9b9790226147a11346e00c@hms.harvard.edu>


Thanks again for everyone's helpful suggestions.
I will try to get back to this later today.

I have to be careful, since I am unfamiliar with large-scale  
programming (mostly a bench virologist, my own sequence analysis  
programs are usually only a few pages of code, with text as the only  
input and output) and I cannot afford to break my existing system. In  
particular, I am using phred/phrap/consed for several important  
sequencing projects and it is -after a good deal of struggle- working  
fine with my existing X11 from the Apple SDK (about which I know  
nothing except at the user level). I am hesitant to mess with this. I  
may try again to compile without X11 (this failed before but may have  
been because of something else I was working on at the time). If this  
works, can one go back and add X11 later, once the kinks have been  
worked out? For now, I would be happy with just text-based sequence  
manipulation.

thanks again
robin



On Mar 31, 2005, at 6:40 AM, Koen van der Drift wrote:

>
> On Mar 30, 2005, at 9:23 PM, Robin Colgrove wrote:
>
>> You have an existing X11 installation in /usr/X11R6 and/or /etc/X11.
>> This package refuses to overwrite these. Remove them, then tell Fink  
>> to
>> install xfree86 again. (The package won't be recompiled.) If you want
>> to keep your X11 installation, install system-xfree86 resp.  
>> system-xtools
>> instead to make this known to Fink's package system.
>>
>
> Sorry that fink is giving you so much problems. It can indeed be  
> frustrating for new users, especially with all the X11 options. If I  
> understand it correctly, you are building xfree86 from fink, but you  
> already have it installed by yourself. I suggest you remove (or  
> better, move it to a temp folder so you can always move it back) the  
> /usr/X11R6 and /etc/X11 directories, and try the fink package again.  
> You have to make sure that you install everyting from the same  
> package, don't mix and match your xfree86 with apple's X11, or fink's  
> xorg. See also this entry in the fink FAQ:
>
> http://fink.sourceforge.net/faq/usage-general.php?phpLang=en#x-options
>
>> dpkg: error processing  
>> /sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/ 
>> xfree86_4.4.0-13_darwin-powerpc.deb (--install):
>
> I see that you are using the stable tree from fink. Emboss 2.10 is so  
> far only available in the unstable tree. This doesn't mean that it is  
> not working, it means that there hasn't been feedback from users that  
> it is working with or without problems. Please keep me informed if you  
> got it to work, since I am the maintainer of the emboss package in  
> fink. If you give me positive feeedback, I can move it to the stable  
> tree.
>
> http://fink.sourceforge.net/faq/usage-fink.php?phpLang=en#unstable
>
>
> Finally, if everything went fine, I can highly recommend the  
> emboss-kaptain package from fink which will give you a very nice GUI  
> in X11.
>
> good luck,
>
> - Koen.
>



From kvddrift at earthlink.net  Thu Mar 31 10:41:07 2005
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Thu, 31 Mar 2005 10:41:07 -0500
Subject: [EMBOSS] More on EMBOSS install on OS X: refuses to overwrite X11
In-Reply-To: <d88d25794e9b9790226147a11346e00c@hms.harvard.edu>
References: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu> <b149de611d71cdea5b437885845aa87a@hms.harvard.edu> <bd2e28683bc7b81f575e459d83174102@earthlink.net> <d88d25794e9b9790226147a11346e00c@hms.harvard.edu>
Message-ID: <67f4be0ec322b07bc201059c01709620@earthlink.net>


On Mar 31, 2005, at 9:46 AM, Robin Colgrove wrote:

> In particular, I am using phred/phrap/consed for several important 
> sequencing projects and it is -after a good deal of struggle- working 
> fine with my existing X11 from the Apple SDK (about which I know 
> nothing except at the user level). I am hesitant to mess with this.

If you have only Apple's X11 and Apple's X11-SDK installed, and no 
other flavors of X (you mentioned in a previous email that you 
installed xfree86), then there should be no problem with fink. I 
suggest you move your current X11 (in /usr/X11R6 and /etc/X11 and 
/Applications/Utilities/X11.app) to eg a temp directory. Then try to 
install a fresh Apple X11 and Apple X11-SDK. Fink should then be able 
to detect that you have an existing X11 package. If you want to restore 
the old X11, just copy them back from the temp directory.  The various 
X11 packages can be very confusing, especially if you have not much 
experience with it, as seems to be in your case. But once you have set 
it up, it works very well.



>  I may try again to compile without X11 (this failed before but may 
> have been because of something else I was working on at the time). If 
> this works, can one go back and add X11 later, once the kinks have 
> been worked out? For now, I would be happy with just text-based 
> sequence manipulation.
>

Indeed, there should probably be a command line version too. Since I am 
the emboss maintainer for fink, I will look into that.


- Koen. 



From robin at hms.harvard.edu  Thu Mar 31 12:30:23 2005
From: robin at hms.harvard.edu (Robin Colgrove)
Date: Thu, 31 Mar 2005 12:30:23 -0500
Subject: [EMBOSS] More on EMBOSS install on OS X without fink or X11 -> does not write executables into /usr/local/share
In-Reply-To: <d88d25794e9b9790226147a11346e00c@hms.harvard.edu>
References: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu> <b149de611d71cdea5b437885845aa87a@hms.harvard.edu> <bd2e28683bc7b81f575e459d83174102@earthlink.net> <d88d25794e9b9790226147a11346e00c@hms.harvard.edu>
Message-ID: <f07fc0f620e922b035729fa0be952127@hms.harvard.edu>



Ok,

I tried again, installing without fink and configuring with the 
--without-x flag.
This time make finishes without errors,
(but with this warning over and over:
ld: warning prebinding disabled because dependent library: 
/usr/local/lib/libnucleus.0.dylib is not prebound)
but still the first test in the tutorial fails

%wossname ->no such file or directory
so
%find / -name "wossname*" -print
finds only
/usr/local/share/EMBOSS/acd/wossname.acd
and in the install directory:
/Users/robin/Desktop/EMBOSS-2.10.0/doc/programs/html/wossname.html
/Users/robin/Desktop/EMBOSS-2.10.0/doc/programs/text/wossname.txt
/Users/robin/Desktop/EMBOSS-2.10.0/emboss/.deps/wossname.Po
/Users/robin/Desktop/EMBOSS-2.10.0/emboss/.libs/wossname
/Users/robin/Desktop/EMBOSS-2.10.0/emboss/acd/wossname.acd
/Users/robin/Desktop/EMBOSS-2.10.0/emboss/wossname
/Users/robin/Desktop/EMBOSS-2.10.0/emboss/wossname.c
/Users/robin/Desktop/EMBOSS-2.10.0/emboss/wossname.o

in /usr/local/share/EMBOSS there is only
acd             data            plstnd5.fnt     plxtnd5.fnt

cd-ing to /Users/robin/Desktop/EMBOSS-2.10.0/emboss finds all the 
executables and
%./wossname
starts up the program, but finds no programs to list.
Trying another program, pepstat, on a test file works fine.

So, now I have a bunch of sequence analysis programs that at least seem 
to work, but are in the wrong place.
I suppose wossname is looking for them in /usr/local/share/EMBOSS.

back to the drawing boards...

robin




From robin at hms.harvard.edu  Thu Mar 31 13:35:50 2005
From: robin at hms.harvard.edu (Robin Colgrove)
Date: Thu, 31 Mar 2005 13:35:50 -0500
Subject: [EMBOSS] More on EMBOSS install on OS X without fink or X11 -> does not write executables into /usr/local/share
In-Reply-To: <f07fc0f620e922b035729fa0be952127@hms.harvard.edu>
References: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu> <b149de611d71cdea5b437885845aa87a@hms.harvard.edu> <bd2e28683bc7b81f575e459d83174102@earthlink.net> <d88d25794e9b9790226147a11346e00c@hms.harvard.edu> <f07fc0f620e922b035729fa0be952127@hms.harvard.edu>
Message-ID: <0b332ee145f305d726c3041d97d1a584@hms.harvard.edu>

Sorry, I should have figured this out sooner myself
but for the benefit of any other newbies unaccustomed to being root:
once I re-ran the install with sudo, everything worked fine (without 
X11).

Now, I will have to go back and figure out about X11...

thanks for all the suggestions.

robin

On Mar 31, 2005, at 12:30 PM, Robin Colgrove wrote:

>
>
> Ok,
>
> I tried again, installing without fink and configuring with the 
> --without-x flag.
> This time make finishes without errors,
> (but with this warning over and over:
> ld: warning prebinding disabled because dependent library: 
> /usr/local/lib/libnucleus.0.dylib is not prebound)
> but still the first test in the tutorial fails
>
> %wossname ->no such file or directory
> so
> %find / -name "wossname*" -print
> finds only
> /usr/local/share/EMBOSS/acd/wossname.acd
> and in the install directory:
> /Users/robin/Desktop/EMBOSS-2.10.0/doc/programs/html/wossname.html
> /Users/robin/Desktop/EMBOSS-2.10.0/doc/programs/text/wossname.txt
> /Users/robin/Desktop/EMBOSS-2.10.0/emboss/.deps/wossname.Po
> /Users/robin/Desktop/EMBOSS-2.10.0/emboss/.libs/wossname
> /Users/robin/Desktop/EMBOSS-2.10.0/emboss/acd/wossname.acd
> /Users/robin/Desktop/EMBOSS-2.10.0/emboss/wossname
> /Users/robin/Desktop/EMBOSS-2.10.0/emboss/wossname.c
> /Users/robin/Desktop/EMBOSS-2.10.0/emboss/wossname.o
>
> in /usr/local/share/EMBOSS there is only
> acd             data            plstnd5.fnt     plxtnd5.fnt
>
> cd-ing to /Users/robin/Desktop/EMBOSS-2.10.0/emboss finds all the 
> executables and
> %./wossname
> starts up the program, but finds no programs to list.
> Trying another program, pepstat, on a test file works fine.
>
> So, now I have a bunch of sequence analysis programs that at least 
> seem to work, but are in the wrong place.
> I suppose wossname is looking for them in /usr/local/share/EMBOSS.
>
> back to the drawing boards...
>
> robin
>
>



From kvddrift at earthlink.net  Wed Mar 30 11:55:36 2005
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Wed, 30 Mar 2005 11:55:36 -0500
Subject: [EMBOSS] OS X install fails with "ld: can't locate file for: -lX11"
In-Reply-To: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu>
References: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu>
Message-ID: <a0a97a3068925551af3b8486698dfba6@earthlink.net>


On Mar 30, 2005, at 11:47 AM, Robin Colgrove wrote:

> Does anyone know what this error means and how to fix it?
>
>

Hi Robin,

Have you considered using fink to install EMBOSS?  Version 2.10 
installs without a problem.

Regarding your X11 error, it could be that you didn't install the X11 
SDK. The X11 SDK package is on one of your Panther CDs (forgot which 
one).


- Koen.




From tmargus at ebc.ee  Sun Mar 13 16:34:12 2005
From: tmargus at ebc.ee (=?ISO-8859-4?Q?T=F5nu_Margus?=)
Date: Sun, 13 Mar 2005 18:34:12 +0200
Subject: [EMBOSS] problems with indexing RDP SSU_RNA  aligned version with dbflat and dbifasta
Message-ID: <20050313162328.A7B6751927@mercury.hgmp.mrc.ac.uk>

Hi, 

 

I fall in to problems when I tried to index alignes SSU_RRNA sequences from
RDP release 9.26  (both fasta and GB format).

Both files are large than 2 GB (fasta is 5GB and is ca 7GB). 

 

It seems to me that dbflat and dbfasta  (EMBOSS rel 2.9) cannot manage with
wiles what are large than 2 GB in my Mandrake Linux 9.2.

 

If this is correct what could be solution?

 

Is it possible to let them index files form stdin?    Someting like   cat
release_9.26_aligned.fasta    | dbfasta   -bla  -bla -blaa  

  

or  must I split it in to  smaller parts than  2GB?

 

If the spliting is only way is there some tool what can do it correctly for
genbanck format?

 

 

 

Thanks in advance

 

T?nu Margus

 

 

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From fernan at iib.unsam.edu.ar  Tue Mar 15 17:36:39 2005
From: fernan at iib.unsam.edu.ar (Fernan Aguero)
Date: Tue, 15 Mar 2005 14:36:39 -0300
Subject: [EMBOSS] EMBOSS 2.10.0 released
In-Reply-To: <200502200004.j1K04J2l014579@bromine.hgmp.mrc.ac.uk>
References: <200502200004.j1K04J2l014579@bromine.hgmp.mrc.ac.uk>
Message-ID: <20050315173639.GC80393@iib.unsam.edu.ar>

+----[ Alan Bleasby <ableasby at hgmp.mrc.ac.uk> (19.Feb.2005 21:09):
|
| EMBOSS 2.10.0 can be downloaded from the following URL:
| 
|    ftp://ftp.rfcgr.mrc.ac.uk/pub/EMBOSS/
| 
| or via the EMBOSS homepage:
| 
|    http://emboss.sourceforge.net
|
+----]

Alan,

I'm now updating the FreeBSD ports to 2.10.0, and noticed
that the new MYEMBOSS-1.0.0.tar.gz can't be found in the
main site nor in any mirror.

Should I wait and include this on the list of embassy
apps? Also, when will be avilable the PHILIPNEW embassy
package?

While we're here, a few minor issues:
i) on the emboss.sf.net main page the latest release is still 2.9.0
ii) what are the requirements for OSs to enter the 'It is
reported to work' category on the 'System requirements'
section of the /download/ page? Maybe FreeBSD can be moved
to this category?

Thanks for the good work,

Fernan


From ableasby at hgmp.mrc.ac.uk  Tue Mar 15 21:58:18 2005
From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby)
Date: Tue, 15 Mar 2005 21:58:18 GMT
Subject: [EMBOSS] EMBOSS 2.10.0 released
Message-ID: <200503152158.j2FLwIg0002323@bromine.hgmp.mrc.ac.uk>

Thanks for the feedback Fernan.
FreeBSD had to slip down the list when your predecessor was
no longer able to do the port (although we did make sure that
EMBOSS compiled on that OS ... it just wasn't packaged in
the FreeBSD style). Thanks for taking that over. We'll adjust
the web pages.

PHYLIPNEW and MYEMBOSS are still undergoing testing. We will be
updating phylipnew before its release. We'd hope to get it
out by July. Myemboss is a developers package rather than an
application so it doesn't need to be provided in any standard
release. However, by July for that too.

Cheers
Alan


From stefanielager at fastmail.ca  Tue Mar 22 13:20:07 2005
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Tue, 22 Mar 2005 13:20:07 +0000 (UTC)
Subject: [EMBOSS] Including exonerate in EMBOSS?
Message-ID: <20050322132008.291CE8613B0@mail.interchange.ca>

Hi,

Has anyone considered including the exonerate alignment algorithm
(Slater & Birney 2005) into EMBOSS? Exonerate could replace most of the
alignment algorithms currently available in EMBOSS, and it's much
faster. Exonerate would probably also benefit, by addition of yet more
output options and integration with current EMBOSS applications.    

Stefanie


Slater GS, Birney E. 
Automated generation of heuristics for biological sequence comparison.
BMC Bioinformatics. 2005 Feb 15;6(1):31.
_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians



From pmr at ebi.ac.uk  Wed Mar 30 15:50:10 2005
From: pmr at ebi.ac.uk (Peter Rice)
Date: Wed, 30 Mar 2005 16:50:10 +0100
Subject: [EMBOSS] Codon usage file improvements
Message-ID: <424ACAB2.8090509@ebi.ac.uk>

A quick check before I make changes to the EMBOSS codon usage files.

EMBOSS includes a set of codon usage files in the emboss/data/CODONS directory 
which are installed for use. The cutgextract program allows administrators to 
install codon usage tables for all species using the cutg database.

The files provided with EMBOSS were from Mike Cherry's 1992 "codonusage" 
database and from a 1994 release of the "transterm" database.

The file names are usually in the format "Egss" where "g" is the first letter 
of the genus, and "ss" is the first 2 letters of the species. Like SwissProt, 
there are a few exceptions (Eyeast for example). The filenames came from these 
databases originally - they were not made up by them EMBOSS team (we only 
added the "E" at the start).

I am modifying cutgextract to include more information in the output files, 
and will update the files in this directory where possible, using data from 
the latest cutg.

Are there any files in emboss/data/CODONS that are particular favourites and 
need to be preserved?

Are there any non-standard .cut filenames in emboss/data/CODONS that will 
cause problems if they are removed?

(Administrators will need to remove the old filenames by hand when they 
install a new version of EMBOSS - we cannot easily remove them automatically).

I will also allow a choice of codon usage file formats - are there any special 
formats that are useful for exchange with other packages?

regards,

Peter Rice




From robin at hms.harvard.edu  Wed Mar 30 16:47:12 2005
From: robin at hms.harvard.edu (Robin Colgrove)
Date: Wed, 30 Mar 2005 11:47:12 -0500
Subject: [EMBOSS] OS X install fails with "ld: can't locate file for: -lX11"
Message-ID: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu>


Hello all,

I am new to the list. Apologies if this is an FAQ. I could not find it 
in the archives.
Anyway, I am running OS X 10.3.8 and downloaded the latest EMBOSS, 
2.10.0.
I followed the instruction for installation, ./configure, then
sudo make
which goes on for a long time, compiling an lot of things, but then 
finally fails with:
[...lots of stuff compiled OK...]
source='aaindexextract.c' object='aaindexextract.o' libtool=no \
DEPDIR=.deps depmode=gcc /bin/sh ../depcomp \
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" 
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" 
-DVERSION=\"2.10.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DX_DISPLAY_MISSING=1 
-DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 
-DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 
-DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 
-DHAVE_MEMMOVE=1 -DHAVE_LIBM=1  -I. -I. -I../nucleus -I../ajax 
-I../plplot  -DAJ_MACOSXLF  -DBENDIAN -DNO_AUTH  -O2 -c 
aaindexextract.c
/bin/sh ../libtool --tag=CC --mode=link gcc  -O2   -o aaindexextract  
aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la 
../ajax/libajax.la ../plplot/libplplot.la -lX11  -lm
mkdir .libs
gcc -O2 -o .libs/aaindexextract aaindexextract.o  
../nucleus/.libs/libnucleus.dylib ../ajax/.libs/libajaxg.dylib 
../ajax/.libs/libajax.dylib ../plplot/.libs/libplplot.dylib -lX11 -lm
ld: can't locate file for: -lX11
make[2]: *** [aaindexextract] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

[...and then exits...]

just to see if it would work, I tried
sudo make install
which installed a lot of things but then failed with:

/bin/sh ../libtool --tag=CC --mode=link gcc  -O2   -o aaindexextract  
aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la 
../ajax/libajax.la ../plplot/libplplot.la -lX11  -lm
gcc -O2 -o .libs/aaindexextract aaindexextract.o  
../nucleus/.libs/libnucleus.dylib ../ajax/.libs/libajaxg.dylib 
../ajax/.libs/libajax.dylib ../plplot/.libs/libplplot.dylib -lX11 -lm
ld: can't locate file for: -lX11
make[2]: *** [aaindexextract] Error 1
make[1]: *** [install-recursive] Error 1
make: *** [install-recursive] Error 1

Hoping it would work anyway, I tried the tutorial and the first example:
%wossname
fails with
tcsh: wossname: Command not found.
even though I see:
/usr/local/share/EMBOSS/acd/wossname.acd

My knowledge of these things is rudimentary, but the error seems to be 
complaining about not finding X11, but that can't be right, since I 
have
X11 1.0 - XFree86 4.3.0
and have been using it for other programs like Phred/Phrap/Consed.

Does anyone know what this error means and how to fix it?

thanks

robin colgrove
department of microbiology
harvard medical school



From andrespinzon at gmail.com  Wed Mar 30 17:22:20 2005
From: andrespinzon at gmail.com (Andres Pinzon)
Date: Wed, 30 Mar 2005 12:22:20 -0500
Subject: [EMBOSS] OS X install fails with "ld: can't locate file for: -lX11"
In-Reply-To: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu>
References: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu>
Message-ID: <8968fc7e05033009225e9aabd4@mail.gmail.com>

On Wed, 30 Mar 2005 11:47:12 -0500, Robin Colgrove
<robin at hms.harvard.edu> wrote:

> My knowledge of these things is rudimentary, but the error seems to be
> complaining about not finding X11, but that can't be right, since I
> have
> X11 1.0 - XFree86 4.3.0
> and have been using it for other programs like Phred/Phrap/Consed.
> 
> Does anyone know what this error means and how to fix it?

Sure, all you have to do is to install the development (devel)
libraries for xfree86, (something like Xfree86-4.3.9-devel.....), some
systems doesnt install this libraries by default, since are not
commonly used, some others dont even provide them (red hat, for
instance).
In fact you have 2 possibilities, the first one is to install the
development packages for your Xfree86 version (as ialready commented),
the other one is to install EMBOSS without X support:
                      ./configure --without-x

With this option you wont have problems with the X stystem but EMBOS
will not be able to plot imges in the X windows system (used by
plotorf, for example).

This is the command i run once i installed the devel packages:

   ./configure --with-pngdriver=/usr/lib/ --prefix=/usr/local/emboss

Ok, i hope this will help you.
-- 
---------
Andr?s Pinz?n [http://www.andrespinzon.com]   
Centro de Bioinformatica, Instituto de Biotecnologia
http://bioinf.ibun.unal.edu.co
Universidad Nacional de Colombia
tel. 3165000 ext. 16961   
GNU/Linux ...para un mundo libre!
----------


From gbottu at ben.vub.ac.be  Wed Mar 30 17:21:18 2005
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Wed, 30 Mar 2005 19:21:18 +0200
Subject: [EMBOSS] CODON USAGE TABLES
Message-ID: <20050330172118.GA14064@bigben.ulb.ac.be>

	Dear Peter, dear all,

A few thoughts on the codon usage tables, now that you are working on 
them.

Do you intend to drop the existing tables from the distribution in favor 
of tables from CUTG ? CUTG has one drawback : the entries for each 
organism/organelle are made from all the genes, without taking account of 
the fact that there exist distinct subpopulations. E.g. in E. coli there 
are the highly expressed genes, the lowly expressed genes and the 
horizontally transferred genes, which have different codon usage. I think 
that in the distribution there are at least for some organisms specific 
files (e.g. Eeco.cut and Eeco_h.cut). The great problem with the files 
from the current distribution is that it is hard to find out which file 
contains what.

There is the issue of the number of files in the face of GUI's. Some GUI's 
for EMBOSS generate a selector from which the user can choose a codon 
usage table. If the complete CUTG has been extracted and installed, this 
does not work well anymore. A selector with more than 10000 entries is not 
convenient and furthermore, in a WWW interface the HTML page takes a 
perceptibly long time to download.
At the BEN site I solved this the following (not necessarily satisfactory) 
way : I modified cutgextract so that it creates files with extension .cutg 
rather than .cut. The interface wEMBOSS only shows the *.cut files in the 
selector. If a user wants to use a CUTG rather than a standard 
distribution file under wEMBOSS, he must first copy it to his project 
using embossdata (at the command line there is no problem).

As formats, it would of course be nice if EMBOSS programs could read and 
write codon usage tables (and other data) in any format, just as they do 
for sequences. Which formats should we support besides what EMBOSS uses 
now ? Is there such a thing as "native" CUTG format (with one entry a 
file) ?. I know about GCG format (not useful for us, but other people 
certainly might want it). There is Staden format. Staden format supports 
also files with 2 tables (codon usage in genes + trinucleotide frequency 
in noncoding DNA) ; what to do with this ? only read the first ? There is 
also the format used by CODEHOP 
(http://blocks.fhcrc.org/blocks/codehop.html). Does 
someone know other formats ?

	Regards,
	Guy Bottu,
	Belgian EMBnet Node
 


From robin at hms.harvard.edu  Thu Mar 31 02:23:21 2005
From: robin at hms.harvard.edu (Robin Colgrove)
Date: Wed, 30 Mar 2005 21:23:21 -0500
Subject: [EMBOSS] More on EMBOSS install on OS X: refuses to overwrite X11
In-Reply-To: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu>
References: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu>
Message-ID: <b149de611d71cdea5b437885845aa87a@hms.harvard.edu>


Many thanks to all who suggested fixes for an OS X emboss install.
Not having time to mix and match, I tried them all. After a few failed  
attempts to try them one by one.

I updated to the latest X11SDK in the Xcode1.5 package.
I updated fink to the latest 0.71 version.
and then I tried using fink to install emboss.

It went on for a couple of _hours_, installing a huge number of things  
but then finally dumped me out, complaining that there is an existing  
X11 distribution and telling me to remove it. This is sort of  
obnoxious, since I use my existing X11 for sequence assembly with  
consed, and it works fine and is important to my work. Fink/emboss  
gives me no assurance that it will not screw up what I have working  
already (and which took me no small amount of effort to get working),  
so I am not about to blithely remove my existing X11 without some way  
to know that I will not mess up what is working now.

I thought maybe everything _but_ X11 got installed, but even the first  
example in the tutorial fails:
[dhc017077:~] robin% wossname
tcsh: wossname: Command not found.
[dhc017077:~] robin% man wossname
No manual entry for wossname

So now I cannot tell whether anything at all is working or what to do  
to debug it. Fink seems to have downloaded, compiled and installed  
hundreds of files on my machine but not given me any working programs.  
Very frustrating.

below are the last few lines of installer output.
Any advice on where to go from here appreciated...

robin

************

dpkg-deb: building package `xfree86-shlibs' in  
`/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/xfree86- 
shlibs_4.4.0-13_darwin-powerpc.deb'.
dpkg -i  
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/ 
xfree86_4.4.0-13_darwin-powerpc.deb  
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/xfree86- 
shlibs_4.4.0-13_darwin-powerpc.deb
Selecting previously deselected package xfree86.
(Reading database ... 4015 files and directories currently installed.)
Unpacking xfree86 (from .../xfree86_4.4.0-13_darwin-powerpc.deb) ...
WARNING: if you compile X11 applications against this XFree86 release,
you will *not* be able to run them if you decide to revert to Apple's
X11 provided with Panther.

You have an existing X11 installation in /usr/X11R6 and/or /etc/X11.
This package refuses to overwrite these. Remove them, then tell Fink to
install xfree86 again. (The package won't be recompiled.) If you want
to keep your X11 installation, install system-xfree86 resp.  
system-xtools
instead to make this known to Fink's package system.

Press Return to continue.

dpkg: error processing  
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/ 
xfree86_4.4.0-13_darwin-powerpc.deb (--install):
  subprocess pre-installation script returned error exit status 1
Selecting previously deselected package xfree86-shlibs.
Unpacking xfree86-shlibs (from  
.../xfree86-shlibs_4.4.0-13_darwin-powerpc.deb) ...

You have an existing X11 installation in /usr/X11R6/lib.
This package refuses to overwrite these. Remove them, then tell Fink to
install xfree86-shlibs again. (The package won't be recompiled.)

Press Return to continue.

dpkg: error processing  
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/xfree86- 
shlibs_4.4.0-13_darwin-powerpc.deb (--install):
  subprocess pre-installation script returned error exit status 1
Errors were encountered while processing:
   
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/ 
xfree86_4.4.0-13_darwin-powerpc.deb
   
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/xfree86- 
shlibs_4.4.0-13_darwin-powerpc.deb
### execution of dpkg failed, exit code 1
Failed: can't batch-install packages:  
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/ 
xfree86_4.4.0-13_darwin-powerpc.deb  
/sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/xfree86- 
shlibs_4.4.0-13_darwin-powerpc.deb


On Mar 30, 2005, at 11:47 AM, Robin Colgrove wrote:

>
> Hello all,
>
> I am new to the list. Apologies if this is an FAQ. I could not find it  
> in the archives.
> Anyway, I am running OS X 10.3.8 and downloaded the latest EMBOSS,  
> 2.10.0.
> I followed the instruction for installation, ./configure, then
> sudo make
> which goes on for a long time, compiling an lot of things, but then  
> finally fails with:
> [...lots of stuff compiled OK...]
> source='aaindexextract.c' object='aaindexextract.o' libtool=no \
> DEPDIR=.deps depmode=gcc /bin/sh ../depcomp \
> gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"  
> -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\"  
> -DVERSION=\"2.10.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1  
> -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1  
> -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1  
> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DX_DISPLAY_MISSING=1  
> -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1  
> -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1  
> -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1  
> -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1  -I. -I. -I../nucleus -I../ajax  
> -I../plplot  -DAJ_MACOSXLF  -DBENDIAN -DNO_AUTH  -O2 -c  
> aaindexextract.c
> /bin/sh ../libtool --tag=CC --mode=link gcc  -O2   -o aaindexextract   
> aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la  
> ../ajax/libajax.la ../plplot/libplplot.la -lX11  -lm
> mkdir .libs
> gcc -O2 -o .libs/aaindexextract aaindexextract.o   
> ../nucleus/.libs/libnucleus.dylib ../ajax/.libs/libajaxg.dylib  
> ../ajax/.libs/libajax.dylib ../plplot/.libs/libplplot.dylib -lX11 -lm
> ld: can't locate file for: -lX11
> make[2]: *** [aaindexextract] Error 1
> make[1]: *** [all-recursive] Error 1
> make: *** [all-recursive] Error 1
>
> [...and then exits...]
>
> just to see if it would work, I tried
> sudo make install
> which installed a lot of things but then failed with:
>
> /bin/sh ../libtool --tag=CC --mode=link gcc  -O2   -o aaindexextract   
> aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la  
> ../ajax/libajax.la ../plplot/libplplot.la -lX11  -lm
> gcc -O2 -o .libs/aaindexextract aaindexextract.o   
> ../nucleus/.libs/libnucleus.dylib ../ajax/.libs/libajaxg.dylib  
> ../ajax/.libs/libajax.dylib ../plplot/.libs/libplplot.dylib -lX11 -lm
> ld: can't locate file for: -lX11
> make[2]: *** [aaindexextract] Error 1
> make[1]: *** [install-recursive] Error 1
> make: *** [install-recursive] Error 1
>
> Hoping it would work anyway, I tried the tutorial and the first  
> example:
> %wossname
> fails with
> tcsh: wossname: Command not found.
> even though I see:
> /usr/local/share/EMBOSS/acd/wossname.acd
>
> My knowledge of these things is rudimentary, but the error seems to be  
> complaining about not finding X11, but that can't be right, since I  
> have
> X11 1.0 - XFree86 4.3.0
> and have been using it for other programs like Phred/Phrap/Consed.
>
> Does anyone know what this error means and how to fix it?
>
> thanks
>
> robin colgrove
> department of microbiology
> harvard medical school
>


From andrespinzon at gmail.com  Thu Mar 31 03:14:35 2005
From: andrespinzon at gmail.com (Andres Pinzon)
Date: Wed, 30 Mar 2005 22:14:35 -0500
Subject: [EMBOSS] More on EMBOSS install on OS X: refuses to overwrite X11
In-Reply-To: <b149de611d71cdea5b437885845aa87a@hms.harvard.edu>
References: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu>
	 <b149de611d71cdea5b437885845aa87a@hms.harvard.edu>
Message-ID: <8968fc7e0503301914488d36b@mail.gmail.com>

On Wed, 30 Mar 2005 21:23:21 -0500, Robin Colgrove
<robin at hms.harvard.edu> wrote:
> 
> Many thanks to all who suggested fixes for an OS X emboss install.
> Not having time to mix and match, I tried them all. After a few failed
> attempts to try them one by one.

Robin, what happened when you tried to configure EMBOSS with the
"--without-x" option? What error did you get?
Did you also tried to install the devel packages?
I had exactly the same problem (in a Linux box) and that was the way i
fixed it. Now my EMBOSS installation runs ok, with wEMBOSS and
EMBOSS::GUI.
-- 
---------
Andr?s Pinz?n [http://www.andrespinzon.com]   
Centro de Bioinformatica, Instituto de Biotecnologia
http://bioinf.ibun.unal.edu.co
Universidad Nacional de Colombia
tel. 3165000 ext. 16961   
GNU/Linux ...para un mundo libre!
----------


From kvddrift at earthlink.net  Thu Mar 31 11:40:59 2005
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Thu, 31 Mar 2005 06:40:59 -0500
Subject: [EMBOSS] More on EMBOSS install on OS X: refuses to overwrite X11
In-Reply-To: <b149de611d71cdea5b437885845aa87a@hms.harvard.edu>
References: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu> <b149de611d71cdea5b437885845aa87a@hms.harvard.edu>
Message-ID: <bd2e28683bc7b81f575e459d83174102@earthlink.net>


On Mar 30, 2005, at 9:23 PM, Robin Colgrove wrote:

> You have an existing X11 installation in /usr/X11R6 and/or /etc/X11.
> This package refuses to overwrite these. Remove them, then tell Fink to
> install xfree86 again. (The package won't be recompiled.) If you want
> to keep your X11 installation, install system-xfree86 resp.  
> system-xtools
> instead to make this known to Fink's package system.
>

Sorry that fink is giving you so much problems. It can indeed be  
frustrating for new users, especially with all the X11 options. If I  
understand it correctly, you are building xfree86 from fink, but you  
already have it installed by yourself. I suggest you remove (or better,  
move it to a temp folder so you can always move it back) the /usr/X11R6  
and /etc/X11 directories, and try the fink package again. You have to  
make sure that you install everyting from the same package, don't mix  
and match your xfree86 with apple's X11, or fink's xorg. See also this  
entry in the fink FAQ:

http://fink.sourceforge.net/faq/usage-general.php?phpLang=en#x-options

> dpkg: error processing  
> /sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/ 
> xfree86_4.4.0-13_darwin-powerpc.deb (--install):

I see that you are using the stable tree from fink. Emboss 2.10 is so  
far only available in the unstable tree. This doesn't mean that it is  
not working, it means that there hasn't been feedback from users that  
it is working with or without problems. Please keep me informed if you  
got it to work, since I am the maintainer of the emboss package in  
fink. If you give me positive feeedback, I can move it to the stable  
tree.

http://fink.sourceforge.net/faq/usage-fink.php?phpLang=en#unstable


Finally, if everything went fine, I can highly recommend the  
emboss-kaptain package from fink which will give you a very nice GUI in  
X11.

good luck,

- Koen.



From robin at hms.harvard.edu  Thu Mar 31 14:46:00 2005
From: robin at hms.harvard.edu (Robin Colgrove)
Date: Thu, 31 Mar 2005 09:46:00 -0500
Subject: [EMBOSS] More on EMBOSS install on OS X: refuses to overwrite X11
In-Reply-To: <bd2e28683bc7b81f575e459d83174102@earthlink.net>
References: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu> <b149de611d71cdea5b437885845aa87a@hms.harvard.edu> <bd2e28683bc7b81f575e459d83174102@earthlink.net>
Message-ID: <d88d25794e9b9790226147a11346e00c@hms.harvard.edu>


Thanks again for everyone's helpful suggestions.
I will try to get back to this later today.

I have to be careful, since I am unfamiliar with large-scale  
programming (mostly a bench virologist, my own sequence analysis  
programs are usually only a few pages of code, with text as the only  
input and output) and I cannot afford to break my existing system. In  
particular, I am using phred/phrap/consed for several important  
sequencing projects and it is -after a good deal of struggle- working  
fine with my existing X11 from the Apple SDK (about which I know  
nothing except at the user level). I am hesitant to mess with this. I  
may try again to compile without X11 (this failed before but may have  
been because of something else I was working on at the time). If this  
works, can one go back and add X11 later, once the kinks have been  
worked out? For now, I would be happy with just text-based sequence  
manipulation.

thanks again
robin



On Mar 31, 2005, at 6:40 AM, Koen van der Drift wrote:

>
> On Mar 30, 2005, at 9:23 PM, Robin Colgrove wrote:
>
>> You have an existing X11 installation in /usr/X11R6 and/or /etc/X11.
>> This package refuses to overwrite these. Remove them, then tell Fink  
>> to
>> install xfree86 again. (The package won't be recompiled.) If you want
>> to keep your X11 installation, install system-xfree86 resp.  
>> system-xtools
>> instead to make this known to Fink's package system.
>>
>
> Sorry that fink is giving you so much problems. It can indeed be  
> frustrating for new users, especially with all the X11 options. If I  
> understand it correctly, you are building xfree86 from fink, but you  
> already have it installed by yourself. I suggest you remove (or  
> better, move it to a temp folder so you can always move it back) the  
> /usr/X11R6 and /etc/X11 directories, and try the fink package again.  
> You have to make sure that you install everyting from the same  
> package, don't mix and match your xfree86 with apple's X11, or fink's  
> xorg. See also this entry in the fink FAQ:
>
> http://fink.sourceforge.net/faq/usage-general.php?phpLang=en#x-options
>
>> dpkg: error processing  
>> /sw/fink/dists/stable/main/binary-darwin-powerpc/x11-system/ 
>> xfree86_4.4.0-13_darwin-powerpc.deb (--install):
>
> I see that you are using the stable tree from fink. Emboss 2.10 is so  
> far only available in the unstable tree. This doesn't mean that it is  
> not working, it means that there hasn't been feedback from users that  
> it is working with or without problems. Please keep me informed if you  
> got it to work, since I am the maintainer of the emboss package in  
> fink. If you give me positive feeedback, I can move it to the stable  
> tree.
>
> http://fink.sourceforge.net/faq/usage-fink.php?phpLang=en#unstable
>
>
> Finally, if everything went fine, I can highly recommend the  
> emboss-kaptain package from fink which will give you a very nice GUI  
> in X11.
>
> good luck,
>
> - Koen.
>



From kvddrift at earthlink.net  Thu Mar 31 15:41:07 2005
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Thu, 31 Mar 2005 10:41:07 -0500
Subject: [EMBOSS] More on EMBOSS install on OS X: refuses to overwrite X11
In-Reply-To: <d88d25794e9b9790226147a11346e00c@hms.harvard.edu>
References: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu> <b149de611d71cdea5b437885845aa87a@hms.harvard.edu> <bd2e28683bc7b81f575e459d83174102@earthlink.net> <d88d25794e9b9790226147a11346e00c@hms.harvard.edu>
Message-ID: <67f4be0ec322b07bc201059c01709620@earthlink.net>


On Mar 31, 2005, at 9:46 AM, Robin Colgrove wrote:

> In particular, I am using phred/phrap/consed for several important 
> sequencing projects and it is -after a good deal of struggle- working 
> fine with my existing X11 from the Apple SDK (about which I know 
> nothing except at the user level). I am hesitant to mess with this.

If you have only Apple's X11 and Apple's X11-SDK installed, and no 
other flavors of X (you mentioned in a previous email that you 
installed xfree86), then there should be no problem with fink. I 
suggest you move your current X11 (in /usr/X11R6 and /etc/X11 and 
/Applications/Utilities/X11.app) to eg a temp directory. Then try to 
install a fresh Apple X11 and Apple X11-SDK. Fink should then be able 
to detect that you have an existing X11 package. If you want to restore 
the old X11, just copy them back from the temp directory.  The various 
X11 packages can be very confusing, especially if you have not much 
experience with it, as seems to be in your case. But once you have set 
it up, it works very well.



>  I may try again to compile without X11 (this failed before but may 
> have been because of something else I was working on at the time). If 
> this works, can one go back and add X11 later, once the kinks have 
> been worked out? For now, I would be happy with just text-based 
> sequence manipulation.
>

Indeed, there should probably be a command line version too. Since I am 
the emboss maintainer for fink, I will look into that.


- Koen. 



From robin at hms.harvard.edu  Thu Mar 31 17:30:23 2005
From: robin at hms.harvard.edu (Robin Colgrove)
Date: Thu, 31 Mar 2005 12:30:23 -0500
Subject: [EMBOSS] More on EMBOSS install on OS X without fink or X11 -> does not write executables into /usr/local/share
In-Reply-To: <d88d25794e9b9790226147a11346e00c@hms.harvard.edu>
References: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu> <b149de611d71cdea5b437885845aa87a@hms.harvard.edu> <bd2e28683bc7b81f575e459d83174102@earthlink.net> <d88d25794e9b9790226147a11346e00c@hms.harvard.edu>
Message-ID: <f07fc0f620e922b035729fa0be952127@hms.harvard.edu>



Ok,

I tried again, installing without fink and configuring with the 
--without-x flag.
This time make finishes without errors,
(but with this warning over and over:
ld: warning prebinding disabled because dependent library: 
/usr/local/lib/libnucleus.0.dylib is not prebound)
but still the first test in the tutorial fails

%wossname ->no such file or directory
so
%find / -name "wossname*" -print
finds only
/usr/local/share/EMBOSS/acd/wossname.acd
and in the install directory:
/Users/robin/Desktop/EMBOSS-2.10.0/doc/programs/html/wossname.html
/Users/robin/Desktop/EMBOSS-2.10.0/doc/programs/text/wossname.txt
/Users/robin/Desktop/EMBOSS-2.10.0/emboss/.deps/wossname.Po
/Users/robin/Desktop/EMBOSS-2.10.0/emboss/.libs/wossname
/Users/robin/Desktop/EMBOSS-2.10.0/emboss/acd/wossname.acd
/Users/robin/Desktop/EMBOSS-2.10.0/emboss/wossname
/Users/robin/Desktop/EMBOSS-2.10.0/emboss/wossname.c
/Users/robin/Desktop/EMBOSS-2.10.0/emboss/wossname.o

in /usr/local/share/EMBOSS there is only
acd             data            plstnd5.fnt     plxtnd5.fnt

cd-ing to /Users/robin/Desktop/EMBOSS-2.10.0/emboss finds all the 
executables and
%./wossname
starts up the program, but finds no programs to list.
Trying another program, pepstat, on a test file works fine.

So, now I have a bunch of sequence analysis programs that at least seem 
to work, but are in the wrong place.
I suppose wossname is looking for them in /usr/local/share/EMBOSS.

back to the drawing boards...

robin




From robin at hms.harvard.edu  Thu Mar 31 18:35:50 2005
From: robin at hms.harvard.edu (Robin Colgrove)
Date: Thu, 31 Mar 2005 13:35:50 -0500
Subject: [EMBOSS] More on EMBOSS install on OS X without fink or X11 -> does not write executables into /usr/local/share
In-Reply-To: <f07fc0f620e922b035729fa0be952127@hms.harvard.edu>
References: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu> <b149de611d71cdea5b437885845aa87a@hms.harvard.edu> <bd2e28683bc7b81f575e459d83174102@earthlink.net> <d88d25794e9b9790226147a11346e00c@hms.harvard.edu> <f07fc0f620e922b035729fa0be952127@hms.harvard.edu>
Message-ID: <0b332ee145f305d726c3041d97d1a584@hms.harvard.edu>

Sorry, I should have figured this out sooner myself
but for the benefit of any other newbies unaccustomed to being root:
once I re-ran the install with sudo, everything worked fine (without 
X11).

Now, I will have to go back and figure out about X11...

thanks for all the suggestions.

robin

On Mar 31, 2005, at 12:30 PM, Robin Colgrove wrote:

>
>
> Ok,
>
> I tried again, installing without fink and configuring with the 
> --without-x flag.
> This time make finishes without errors,
> (but with this warning over and over:
> ld: warning prebinding disabled because dependent library: 
> /usr/local/lib/libnucleus.0.dylib is not prebound)
> but still the first test in the tutorial fails
>
> %wossname ->no such file or directory
> so
> %find / -name "wossname*" -print
> finds only
> /usr/local/share/EMBOSS/acd/wossname.acd
> and in the install directory:
> /Users/robin/Desktop/EMBOSS-2.10.0/doc/programs/html/wossname.html
> /Users/robin/Desktop/EMBOSS-2.10.0/doc/programs/text/wossname.txt
> /Users/robin/Desktop/EMBOSS-2.10.0/emboss/.deps/wossname.Po
> /Users/robin/Desktop/EMBOSS-2.10.0/emboss/.libs/wossname
> /Users/robin/Desktop/EMBOSS-2.10.0/emboss/acd/wossname.acd
> /Users/robin/Desktop/EMBOSS-2.10.0/emboss/wossname
> /Users/robin/Desktop/EMBOSS-2.10.0/emboss/wossname.c
> /Users/robin/Desktop/EMBOSS-2.10.0/emboss/wossname.o
>
> in /usr/local/share/EMBOSS there is only
> acd             data            plstnd5.fnt     plxtnd5.fnt
>
> cd-ing to /Users/robin/Desktop/EMBOSS-2.10.0/emboss finds all the 
> executables and
> %./wossname
> starts up the program, but finds no programs to list.
> Trying another program, pepstat, on a test file works fine.
>
> So, now I have a bunch of sequence analysis programs that at least 
> seem to work, but are in the wrong place.
> I suppose wossname is looking for them in /usr/local/share/EMBOSS.
>
> back to the drawing boards...
>
> robin
>
>



From kvddrift at earthlink.net  Wed Mar 30 16:55:36 2005
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Wed, 30 Mar 2005 11:55:36 -0500
Subject: [EMBOSS] OS X install fails with "ld: can't locate file for: -lX11"
In-Reply-To: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu>
References: <4abaf6654e1bcdae0dac82b696e902ed@hms.harvard.edu>
Message-ID: <a0a97a3068925551af3b8486698dfba6@earthlink.net>


On Mar 30, 2005, at 11:47 AM, Robin Colgrove wrote:

> Does anyone know what this error means and how to fix it?
>
>

Hi Robin,

Have you considered using fink to install EMBOSS?  Version 2.10 
installs without a problem.

Regarding your X11 error, it could be that you didn't install the X11 
SDK. The X11 SDK package is on one of your Panther CDs (forgot which 
one).


- Koen.