From gbottu at vub.ac.be  Fri Jul  6 04:40:46 2007
From: gbottu at vub.ac.be (Guy Bottu)
Date: Fri, 06 Jul 2007 10:40:46 +0200
Subject: [EMBOSS] MRS 3 as EMBOSS sequence access mechanism
Message-ID: <468E000E.5020201@vub.ac.be>

	Dear all,

The MRS servers are shifting from version 2 to version 3. A result is that the 
EMBOSS sequence access mechanism "mrs" does not work anymore. The reason is that 
  the URL to be generated by the software is not anymore something like
http://mrs.cmbi.kun.nl/mrs/cgi-bin/mrs.cgi?db=sprot%2Btrembl&query=id:papa1_carpa&format=entry&exp=1&save_to=text/plain
but
http://mrs.cmbi.kun.nl/mrs-3/plain.do?db=uniprot&id=papa1_carpa
It is not possible to search several databanks at the same time, but MRS 3 has 
composite indexes for e.g. uniprot (=sprot+trembl) or embl (=nonredundant 
release + updates). It is also impossible to make a query with wild cards. A 
suppementary problem is that the MRS WWW server wants to set a cookie.

Do you think the next release of EMBOSS could support MRS 3 (maybe, in the 
tradition of backward compatibility, have both "mrs" and "mrs3" access methods)?

And are some of you really using MRS WWW as access sequence access mechanism for 
EMBOSS ?

	Regards,
	Guy Bottu,
	Belgian EMBnet Node

From pmr at ebi.ac.uk  Fri Jul  6 05:12:30 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 06 Jul 2007 10:12:30 +0100
Subject: [EMBOSS] [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E000E.5020201@vub.ac.be>
References: <468E000E.5020201@vub.ac.be>
Message-ID: <468E077E.5080706@ebi.ac.uk>

Guy Bottu wrote:

> Do you think the next release of EMBOSS could support MRS 3 (maybe, in the 
> tradition of backward compatibility, have both "mrs" and "mrs3" access methods)?

Tricky - today is my last day for making changes before going on vacation until 
the release!

But yes I can do it. Is mrs3 the best name? Probably it is, because the URL now 
contains "mrs-3" :-)

Peter

From pmr at ebi.ac.uk  Fri Jul  6 05:20:47 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 06 Jul 2007 10:20:47 +0100
Subject: [EMBOSS] [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E000E.5020201@vub.ac.be>
References: <468E000E.5020201@vub.ac.be>
Message-ID: <468E096F.70102@ebi.ac.uk>

Guy Bottu wrote:

> It is not possible to search several databanks at the same time, but MRS 3 has 
> composite indexes for e.g. uniprot (=sprot+trembl) or embl (=nonredundant 
> release + updates). It is also impossible to make a query with wild cards. A 
> suppementary problem is that the MRS WWW server wants to set a cookie.

We do not handle cookies. MRS3 will have to work without them. It appears it does.

How does MRS3 search for other fields (accession, etc.)?

Where is the MRS server documentation??? I found no documentation of the URL 
syntax or query fields at the CMBI server.

Peter

From pmr at ebi.ac.uk  Fri Jul  6 05:31:36 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 06 Jul 2007 10:31:36 +0100
Subject: [EMBOSS] [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E000E.5020201@vub.ac.be>
References: <468E000E.5020201@vub.ac.be>
Message-ID: <468E0BF8.4030801@ebi.ac.uk>

Guy Bottu wrote:
> The MRS servers are shifting from version 2 to version 3. A result is that the 
> EMBOSS sequence access mechanism "mrs" does not work anymore. The reason is that 
>   the URL to be generated by the software is not anymore something like
> http://mrs.cmbi.kun.nl/mrs/cgi-bin/mrs.cgi?db=sprot%2Btrembl&query=id:papa1_carpa&format=entry&exp=1&save_to=text/plain
> but
> http://mrs.cmbi.kun.nl/mrs-3/plain.do?db=uniprot&id=papa1_carpa

Hah .. that works from wget but when I try that URL within EMBOSS I get nonsense 
back. The web page returns is a 302 error saying:

The document has moved <a 
href="http://mrs.cmbi.ru.nl/mrs-3/?db=embl&amp;id=x13776Host:">here</a>

with an href of http://mrs.cmbi.ru.nl/mrs-3/?db=embl&amp;id=x13776Host:
(yes, with Host: at the end)


> Do you think the next release of EMBOSS could support MRS 3 (maybe, in the 
> tradition of backward compatibility, have both "mrs" and "mrs3" access methods)?

I will add an MRS3 method. Whether it will work before EMBOSS 5.1.0 is another 
question :-)

Peter

From pmr at ebi.ac.uk  Fri Jul  6 06:13:58 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 06 Jul 2007 11:13:58 +0100
Subject: [EMBOSS] [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E000E.5020201@vub.ac.be>
References: <468E000E.5020201@vub.ac.be>
Message-ID: <468E15E6.1030609@ebi.ac.uk>

Guy Bottu wrote:
> 	Dear all,
> 
> The MRS servers are shifting from version 2 to version 3. A result is that the 
> EMBOSS sequence access mechanism "mrs" does not work anymore. The reason is that 
>   the URL to be generated by the software is not anymore something like
> http://mrs.cmbi.kun.nl/mrs/cgi-bin/mrs.cgi?db=sprot%2Btrembl&query=id:papa1_carpa&format=entry&exp=1&save_to=text/plain
> but
> http://mrs.cmbi.kun.nl/mrs-3/plain.do?db=uniprot&id=papa1_carpa

Hmmm ... I have something working.

The MRS3 server absolutely requires HTTP/1.x on the GET line.

The MRS2 server was happy without it (though I am not sure why it was the only 
EMBOSS method that did not use it)

Peter

From gbottu at vub.ac.be  Mon Jul  9 03:53:25 2007
From: gbottu at vub.ac.be (Guy Bottu)
Date: Mon, 09 Jul 2007 09:53:25 +0200
Subject: [EMBOSS] [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E096F.70102@ebi.ac.uk>
References: <468E000E.5020201@vub.ac.be> <468E096F.70102@ebi.ac.uk>
Message-ID: <4691E975.7050500@vub.ac.be>

Peter Rice wrote:
> How does MRS3 search for other fields (accession, etc.)

Alas, with MRS2 you could write a single URL to perform a query and then
retrieve the result as plain text. With MRS3 this has become impossible,
because there are now separate programs. Could EMBOSS eventually first
ask for a query.do, parse the reply and then ask for a plain.do ?
Or you could consider using the Web services instead. I have no 
experience with the Web services under MRS3 ; I will in the coming weeks 
try to get informed.

> Where is the MRS server documentation??? I found no documentation of the URL 
> syntax or query fields at the CMBI server.

There is no documentation for the moment. Well, let's not blame dear 
Maarten, he is alone in his corner with a big development project...

You can however find a list of available databanks, with for each 
databank the available field shortnames. It is possible to write an URL
like ..../mrs-3/query.do?db=uniprot&query=id:papa?_carpa|ac:papa?_carpa

	Guy



From pmr at ebi.ac.uk  Sun Jul  8 10:22:00 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Sun, 08 Jul 2007 15:22:00 +0100
Subject: [EMBOSS] [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <4691E975.7050500@vub.ac.be>
References: <468E000E.5020201@vub.ac.be> <468E096F.70102@ebi.ac.uk>
	<4691E975.7050500@vub.ac.be>
Message-ID: <4690F308.2000108@ebi.ac.uk>

Guy Bottu wrote:
> Alas, with MRS2 you could write a single URL to perform a query and then
> retrieve the result as plain text. With MRS3 this has become impossible,
> because there are now separate programs. Could EMBOSS eventually first
> ask for a query.do, parse the reply and then ask for a plain.do ?
> Or you could consider using the Web services instead. I have no 
> experience with the Web services under MRS3 ; I will in the coming weeks 
> try to get informed.

Yes ... we already do something like that for Entrez.

> There is no documentation for the moment. Well, let's not blame dear 
> Maarten, he is alone in his corner with a big development project...
> 
> You can however find a list of available databanks, with for each 
> databank the available field shortnames. It is possible to write an URL
> like ..../mrs-3/query.do?db=uniprot&query=id:papa?_carpa|ac:papa?_carpa

Thanks. The query access will now have to wait for EMBOSS 5.1.0. The 
basic ID retrieval is in the 5.0.0 release.

regards,

Peter

From charles-listes-emboss at plessy.org  Sun Jul  8 10:02:57 2007
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Sun, 8 Jul 2007 23:02:57 +0900
Subject: [EMBOSS] Antwort:  Manpage generator
In-Reply-To: <OFEA4A36A9.0EB51F74-ONC12571DF.00259DD5-C12571DF.00264720@schering.de>
References: <20060904042850.GC14634@kunpuu.plessy.org>
	<OFEA4A36A9.0EB51F74-ONC12571DF.00259DD5-C12571DF.00264720@schering.de>
Message-ID: <20070708140257.GA5423@kunpuu.plessy.org>

> Charles Plessy schrieb am 04/09/2006 06:28:50:
> > 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).

Le Mon, Sep 04, 2006 at 08:57:54AM +0200, David.Bauer at SCHERING.DE a ?crit :
> 
> 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.

Dear all,

Thanks do David's suggestion, I managed to write a manpage generator for
EMBOSS programs. It uses the EMBOSS::ACD library (which we ship in
Debian in the package libemboss-acd-perl) to create a docbook XML
document, which is transformed into a manpage with the xsltproc program.
The reason why the generator does not directly write the manpage is
simply that I do not know the nroff syntax.

You can download it from the following URI:
http://svn.debian.org/wsvn/pkg-emboss/emboss/trunk/debian/acd2docbook.pl?op=file&rev=0&sc=0

I have put a couple of examples manpages on my personal website in the
following directory:
http://charles.plessy.org/debian/emboss/

I intend to distribute manpages for all emboss programs in the Debian
package which will be updated after the release of EMBOSS 5.0

Have a nice day,

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

From Richard.Rothery at ualberta.ca  Mon Jul  9 18:29:56 2007
From: Richard.Rothery at ualberta.ca (Richard Rothery)
Date: Mon, 9 Jul 2007 16:29:56 -0600
Subject: [EMBOSS] FW: Ebi_blast and Ebi_tmhmm....
Message-ID: <000501c7c278$ad50b480$5e068081@Nordegg>

Hi,

 

I am trying to install the Ebi_blast (
<http://oryx.ulb.ac.be/embosshelp/ebi_blast.html>
http://oryx.ulb.ac.be/embosshelp/ebi_blast.html) and Ebi_tmhmm (
<http://oryx.ulb.ac.be/embosshelp/ebi_tmhmm.html>
http://oryx.ulb.ac.be/embosshelp/ebi_tmhmm.html) programs or add them to
my EMBOSS installation, and have had not success. Are these part of the
latest release? I think I have version 4.1. Are these perl scripts?

 

Thanks!

 

Richard A. Rothery

 

###############################################

CIHR Membrane Protein Research Group,

Department of Biochemistry, University of Alberta,

Edmonton T6G 2H7

Ph. (780) 492-2229 Fax. (780) 492-0886

###############################################

 


From uludag at ebi.ac.uk  Tue Jul 10 05:03:32 2007
From: uludag at ebi.ac.uk (Mahmut Uludag)
Date: Tue, 10 Jul 2007 10:03:32 +0100
Subject: [EMBOSS] FW: Ebi_blast and Ebi_tmhmm....
In-Reply-To: <000501c7c278$ad50b480$5e068081@Nordegg>
References: <000501c7c278$ad50b480$5e068081@Nordegg>
Message-ID: <1184058212.5690.4.camel@emboss2.ebi.ac.uk>


> I am trying to install the Ebi_blast (
> <http://oryx.ulb.ac.be/embosshelp/ebi_blast.html>
> http://oryx.ulb.ac.be/embosshelp/ebi_blast.html) and Ebi_tmhmm (
> <http://oryx.ulb.ac.be/embosshelp/ebi_tmhmm.html>
> http://oryx.ulb.ac.be/embosshelp/ebi_tmhmm.html) programs or add them to
> my EMBOSS installation, and have had not success. Are these part of the
> latest release?

I have searched my EMBOSS-4.1 and EMBOSS-CVS installations for an acd
file for the above applications. Finding no acd files I can say that
they are not standard applications in the latest release.

Regards,
Mahmut



From david.bauer at bayerhealthcare.com  Tue Jul 10 05:11:19 2007
From: david.bauer at bayerhealthcare.com (david.bauer at bayerhealthcare.com)
Date: Tue, 10 Jul 2007 11:11:19 +0200
Subject: [EMBOSS] FW: Ebi_blast and Ebi_tmhmm....
In-Reply-To: <1184058212.5690.4.camel@emboss2.ebi.ac.uk>
Message-ID: <OFAEC01053.7D958CB4-ONC1257314.00325CAA-C1257314.00327A9C@schering.de>

They are part of "wrappers4EMBOSS".
More information you can find at the wemboss site
http://www.wemboss.org/

Cheers,
David.

emboss-bounces at lists.open-bio.org schrieb am 10/07/2007 11:03:32:

> 
> > I am trying to install the Ebi_blast (
> > <http://oryx.ulb.ac.be/embosshelp/ebi_blast.html>
> > http://oryx.ulb.ac.be/embosshelp/ebi_blast.html) and Ebi_tmhmm (
> > <http://oryx.ulb.ac.be/embosshelp/ebi_tmhmm.html>
> > http://oryx.ulb.ac.be/embosshelp/ebi_tmhmm.html) programs or add them 
to
> > my EMBOSS installation, and have had not success. Are these part of 
the
> > latest release?
> 
> I have searched my EMBOSS-4.1 and EMBOSS-CVS installations for an acd
> file for the above applications. Finding no acd files I can say that
> they are not standard applications in the latest release.
> 
> Regards,
> Mahmut
> 
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss


From ajb at ebi.ac.uk  Sun Jul 15 04:05:54 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Sun, 15 Jul 2007 09:05:54 +0100 (BST)
Subject: [EMBOSS] EMBOSS 5.0.0 released
Message-ID: <55352.81.98.241.17.1184486754.squirrel@webmail.ebi.ac.uk>

1) UNIX

EMBOSS 5.0.0 for UNIXen is now available from the usual ftp server i.e.

       ftp://emboss.open-bio.org/pub/EMBOSS/

as the file EMBOSS-5.0.0.tar.gz . The EMBASSY packages are available
in the same directory. Remember that EMBASSY packages are tailored for
each major release of EMBASSY: do not try to reuse versions from
previous EMBOSS releases.

The sourceforge web pages will be updated tomorrow to show version 5
applications by default. For now they can be accessed explicitly at:
http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/

2) Windows

The Microsoft Windows version is now called mEMBOSS and installs with
a standalone version of Jemboss as a GUI; command line gurus can still
use a command window of course. You must first install Java from
java.sun.com (or java.com) and the vcredist_x86.exe file from the
EMBOSS ftp server or the Microsoft web site (N.B. the latter file is a
new version with the current release, previous releases from the ftp
server will not work). mEMBOSS and vcredist_x86.exe are available in:

       ftp://emboss.open-bio.org/pub/EMBOSS/windows/

Please use the name mEMBOSS (not EMBOSS or EMBOSSWIN) when asking any
questions about the Windows version on the EMBOSS mailing lists.
mEMBOSS has been developed under XP and tested under XP and VISTA, though
it will likely work under several other Windows versions.

3) Changes
See the ChangeLog file

4) Support libraries

UNIX users who use the optional PNG graphics should check that they
have a GD version 2 library (homepage www.libgd.org) installed. GD v1
libraries will not work correctly with EMBOSS 5.0.0. EMBOSS now uses
both PNG and GIF routines from the GD library. EMBOSS has been tested
using GD versions 2.0.33, 2.0.34 and 2.0.35, though some older version
2 libraries should also work.


Alan



From ajb at ebi.ac.uk  Mon Jul 16 06:56:24 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Mon, 16 Jul 2007 11:56:24 +0100 (BST)
Subject: [EMBOSS] New mEMBOSS on ftp server
Message-ID: <41376.81.98.241.17.1184583384.squirrel@webmail.ebi.ac.uk>

A new version of mEMBOSS-5.0.0-setup.exe has been put on the
ftp server (filename unchanged as it is just an enhancement).

It had been noticed that the original version only worked if
your Java was up-to-date (1.6 u2). This new version should also
work with Java 1.4 and Java 1.5. Furthermore, it will auto-detect
the Java location and halt installation if Java is not found.

Alan



From christian.bolliger at id.unizh.ch  Mon Jul 16 11:26:34 2007
From: christian.bolliger at id.unizh.ch (Christian Bolliger)
Date: Mon, 16 Jul 2007 17:26:34 +0200
Subject: [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif support
Message-ID: <469B8E2A.50103@id.unizh.ch>

Dear EMBOSS maintainer

Compilation of EMBOSS 5.0.0 on SLES9 (with all graphical devel libs) fails, while linking:

gcc -O2 -D__amd64__ -o .libs/aaindexextract aaindexextract.o  ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so
../ajax/.libs/libajax.so ../plplot/.libs/libeplplot.so -L/usr/X11R6/lib64 /usr/lib64/libgd.so -L/usr/lib64 -lXpm -lX11
/usr/lib64/libjpeg.so /usr/lib64/libfreetype.so -lpng12 -lpng -lz -lm  -Wl,--rpath -Wl,/usr/local/emboss5/lib

../plplot/.libs/libeplplot.so: undefined reference to `gdImageGifPtr'

Configuration:
./configure --prefix=/usr/local/emboss5

It seems for me that EMBOSS 5.0.0 is looking for GIF support despite of the fact that newer Versions of
gd don't support gif anymore (cf. README line 65).

Is there any workarround for the problem (I don't bother changing code)?

Best regards
Christian
-- 
=============================================================================
Christian Bolliger
IT Services                      | http://www.id.uzh.ch/
Central Systems / HPC   	 | http://www.matterhorn.uzh.ch/
University of  Zuerich           | E-Mail: christian.bolliger at id.uzh.ch
Winterthurerstr. 190             | Tel: +41 (0)1 63 56775
CH-8057 Zuerich; Switzerland     | Fax: +41 (0)1 63 54505
Mime/S CA:                https://www.ca.unizh.ch/client/


From ajb at ebi.ac.uk  Mon Jul 16 12:23:47 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Mon, 16 Jul 2007 17:23:47 +0100 (BST)
Subject: [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif support
In-Reply-To: <469B8E2A.50103@id.unizh.ch>
References: <469B8E2A.50103@id.unizh.ch>
Message-ID: <57855.81.98.241.17.1184603027.squirrel@webmail.ebi.ac.uk>

Dear Christian,

Support for GIF was restored in gd 2.0.28 on July 21st, 2004. So, as
mentioned in the announcement, just install an up-to-date gd2 on SLES 9
and the compilation will work.

I've updated the development version of README to reflect this.

Alan



> Dear EMBOSS maintainer
>
> Compilation of EMBOSS 5.0.0 on SLES9 (with all graphical devel libs)
> fails, while linking:
>
> gcc -O2 -D__amd64__ -o .libs/aaindexextract aaindexextract.o
> ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so
> ../ajax/.libs/libajax.so ../plplot/.libs/libeplplot.so -L/usr/X11R6/lib64
> /usr/lib64/libgd.so -L/usr/lib64 -lXpm -lX11
> /usr/lib64/libjpeg.so /usr/lib64/libfreetype.so -lpng12 -lpng -lz -lm
> -Wl,--rpath -Wl,/usr/local/emboss5/lib
>
> ../plplot/.libs/libeplplot.so: undefined reference to `gdImageGifPtr'
>
> Configuration:
> ./configure --prefix=/usr/local/emboss5
>
> It seems for me that EMBOSS 5.0.0 is looking for GIF support despite of
> the fact that newer Versions of
> gd don't support gif anymore (cf. README line 65).
>
> Is there any workarround for the problem (I don't bother changing code)?
>
> Best regards
> Christian
> --
> =============================================================================
> Christian Bolliger
> IT Services                      | http://www.id.uzh.ch/
> Central Systems / HPC   	 | http://www.matterhorn.uzh.ch/
> University of  Zuerich           | E-Mail: christian.bolliger at id.uzh.ch
> Winterthurerstr. 190             | Tel: +41 (0)1 63 56775
> CH-8057 Zuerich; Switzerland     | Fax: +41 (0)1 63 54505
> Mime/S CA:                https://www.ca.unizh.ch/client/
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



From virtuellefestplatte at gmx.net  Tue Jul 17 01:50:30 2007
From: virtuellefestplatte at gmx.net (Sascha Engel)
Date: Tue, 17 Jul 2007 07:50:30 +0200
Subject: [EMBOSS] Installationproblem emboss-explorer
Message-ID: <20070717055030.195460@gmx.net>

Hi,

I have installed EMBOSS-5.0.0 without any problems and now I try to install emboss-explorer on suse 9.2 (i586).

Unfortunately I get an early error:

Checking if your kit is complete...
Looks good
MakeMaker FATAL: prerequisites not found (Parse::RecDescent 1.9)

        Please install these modules first and rerun 'perl Makefile.PL'.

As far as I know there is no Parse::RecDescent 1.9 - package available for Suse 9.2. I tried to install the fedora package (1.94), but without success.
Anyone went through this before? 

Thanks for helping

Sascha







-- 
Psssst! Schon vom neuen GMX MultiMessenger geh?rt?
Der kanns mit allen: http://www.gmx.net/de/go/multimessenger

From dksamuel at gmail.com  Tue Jul 17 03:16:33 2007
From: dksamuel at gmail.com (Duleep Samuel)
Date: Tue, 17 Jul 2007 12:46:33 +0530
Subject: [EMBOSS] JEMBOSS and mEMBOSS works well on WIN XP Thanks
In-Reply-To: <a0bf33d50707170015y4aeeab5ah2129519a975ffb0c@mail.gmail.com>
References: <a0bf33d50707170009t2819a11ale53403890d73e515@mail.gmail.com>
	<a0bf33d50707170015y4aeeab5ah2129519a975ffb0c@mail.gmail.com>
Message-ID: <a0bf33d50707170016q2d0dd482kd23e3af3d9567027@mail.gmail.com>

Dear all, very happy to have used JEMBOSS and mEMBOSS on WIN XP for 4 hrs
yesterday, real nice program, I remembered the days when I tried to use
EMBOSS GUI with Vigyaan CD, NERC DVD (bootable Knoppix), other GUIs,
miserably failed to load JEMBOSS, and EMBOSS on linux.then EMBOSS 4 on win
XP with its command line, where I typed till my fingers got worn out.
Dreamed of a GUI, Thanks from a grateful user to the great team which made
JEMBOSS and mEMBOSS on WIN XP, with regards Samuel, India.

From scott at cs.wits.ac.za  Tue Jul 17 03:01:42 2007
From: scott at cs.wits.ac.za (Scott Hazelhurst)
Date: Tue, 17 Jul 2007 10:01:42 +0300
Subject: [EMBOSS] EST clustering program
Message-ID: <20070717065805.M59277@cs.wits.ac.za>



One of the applications listed in the suggested list for EMBOSS is a program that does
clustering. We've been working on such a program with collaborators (mainly for ESTs)
and we've recently developed an EMBOSS wrapper for it. Is there any way of making it
available to the community?

Scott


---- Scott Hazelhurst ------------------------  scott at cs.wits.ac.za --------
Bioinformatics & Computer Science, University of the Witwatersrand,
Johannesburg, 2050 Wits, South Africa  +27 11 717-6181  fax: +27 11 717-6199


From ajb at ebi.ac.uk  Tue Jul 17 04:00:36 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Tue, 17 Jul 2007 09:00:36 +0100 (BST)
Subject: [EMBOSS] EST clustering program
In-Reply-To: <20070717065805.M59277@cs.wits.ac.za>
References: <20070717065805.M59277@cs.wits.ac.za>
Message-ID: <43677.81.98.241.17.1184659236.squirrel@webmail.ebi.ac.uk>

Dear Scott,

Sounds good.
The usual route would be to submit it to the
emboss-submit at emboss.open-bio.org list (which will reach all
members of the EMBOSS core team) and then communicate with
whoever gets in touch with you. These days we'd tend to make wrappers
available as EMBASSY packages.

Alan


>
>
> One of the applications listed in the suggested list for EMBOSS is a
> program that does
> clustering. We've been working on such a program with collaborators
> (mainly for ESTs)
> and we've recently developed an EMBOSS wrapper for it. Is there any way of
> making it
> available to the community?
>
> Scott
>
>
> ---- Scott Hazelhurst ------------------------  scott at cs.wits.ac.za
> --------
> Bioinformatics & Computer Science, University of the Witwatersrand,
> Johannesburg, 2050 Wits, South Africa  +27 11 717-6181  fax: +27 11
> 717-6199
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



From rvijayasatya at ncifcrf.gov  Tue Jul 17 17:41:24 2007
From: rvijayasatya at ncifcrf.gov (Ravi Vijaya Satya)
Date: Tue, 17 Jul 2007 17:41:24 -0400
Subject: [EMBOSS] Database too lare for dbifasta
Message-ID: <000001c7c8bb$392f28e0$34572b81@0093Ravi>

Hello,

I am trying to index a large fasta file using dbifasta. He file is 18+GB in
size. Indexing with dbifasta was working fine with EMBOSS-4.0.0. However,
with 4.1.0 or 5.0.0, it complains that the file is 'too large for DBI
indexing. Any suggestions other than switching back to 4.0.0? 

Thanks,
Ravi



From georgios at biotek.uio.no  Wed Jul 18 03:23:28 2007
From: georgios at biotek.uio.no (George Magklaras)
Date: Wed, 18 Jul 2007 09:23:28 +0200
Subject: [EMBOSS] Database too lare for dbifasta
In-Reply-To: <000001c7c8bb$392f28e0$34572b81@0093Ravi>
References: <000001c7c8bb$392f28e0$34572b81@0093Ravi>
Message-ID: <469DBFF0.3020608@biotek.uio.no>

This comes from the nucleus library embdbi.c file.

if(ajFileLength(name) > (ajlong) INT_MAX)
           ajDie("File '%S' too large for DBI indexing", name);


INT_MAX is normally something like #  define INT_MAX       2147483647
, as defined by your /usr/include/limits.h file.

In plain English, this means that you will have to split your flat input 
data files so they are smaller than 2 Gigs. For EMBL database raw files 
, the EMBOSS distribution includes now the 'emblsplit.pl' file , under 
the scripts/ subdirectory. This script splits an #EMBL file (.dat)# your 
pass it into < 2 Gig chunks. This won't work for fasta files, it works 
only for EMBL format so you will have to split your 18 Gigs fasta input 
by other means.

In previous versions of EMBOSS (4.0.0), the DBI formatting appear to 
work, but the emboss index was not right, if your flat input file 
exceeded 2 Gigs. At least, I had problems with indexing EMBL format 
files larger than 2 Gigs and the dbiflat program.

Question to the developers:

Why INT_MAX (signed)? Why not unsigned UINT_MAX (to raise it a bit) or 
another raised limit? It is a bit of an overhead to have to go through 
the file split stage.

Best Regards,
GM

Ravi Vijaya Satya wrote:
> Hello,
> 
> I am trying to index a large fasta file using dbifasta. He file is 18+GB in
> size. Indexing with dbifasta was working fine with EMBOSS-4.0.0. However,
> with 4.1.0 or 5.0.0, it complains that the file is 'too large for DBI
> indexing. Any suggestions other than switching back to 4.0.0? 
> 
> Thanks,
> Ravi
> 
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
> 

-- 
--
George Magklaras

Senior Computer Systems Engineer/UNIX Systems Administrator
EMBnet Technical Management Board
The Biotechnology Centre of Oslo,
University of Oslo
http://www.biotek.uio.no/

EMBnet Norway:	http://www.no.embnet.org/

From ajb at ebi.ac.uk  Wed Jul 18 03:45:24 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 18 Jul 2007 08:45:24 +0100 (BST)
Subject: [EMBOSS] Database too lare for dbifasta
In-Reply-To: <000001c7c8bb$392f28e0$34572b81@0093Ravi>
References: <000001c7c8bb$392f28e0$34572b81@0093Ravi>
Message-ID: <54178.81.98.241.17.1184744724.squirrel@webmail.ebi.ac.uk>

Hello Ravi,

For files >2Gb you should use the dbx* applications for indexing e.g.
dbxfasta. It is likely that dbifasta in EMBOSS 4.0.0 just appeared
to work for large files but that entries past the 2Gb limit would
not be correctly retrieved.

HTH

Alan

> Hello,
>
> I am trying to index a large fasta file using dbifasta. He file is 18+GB
> in
> size. Indexing with dbifasta was working fine with EMBOSS-4.0.0. However,
> with 4.1.0 or 5.0.0, it complains that the file is 'too large for DBI
> indexing. Any suggestions other than switching back to 4.0.0?
>
> Thanks,
> Ravi
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



From georgios at biotek.uio.no  Wed Jul 18 05:30:32 2007
From: georgios at biotek.uio.no (George Magklaras)
Date: Wed, 18 Jul 2007 11:30:32 +0200
Subject: [EMBOSS] Database too lare for dbifasta
In-Reply-To: <54178.81.98.241.17.1184744724.squirrel@webmail.ebi.ac.uk>
References: <000001c7c8bb$392f28e0$34572b81@0093Ravi>
	<54178.81.98.241.17.1184744724.squirrel@webmail.ebi.ac.uk>
Message-ID: <469DDDB8.5080005@biotek.uio.no>



ajb at ebi.ac.uk wrote:
 > Hello Ravi,
 >
 > For files >2Gb you should use the dbx* applications for indexing e.g.
 > dbxfasta.


Is it possible to highlight this in the EMBOSS manuals somehow? 
Application manual pages for the dbx utilities that mention the over 2 
Gbyte capability do of course exist, but the 2G limit is not mentioned 
in the respective manual pages of the dbi utils ('Known Bugs' for 
instance). So, if you have someone that reads the admin manual, he/she 
goes to dbi and not the dbx utils by default.

(If such a reference exists I apologize, but I can't see it. My comments 
refer to 'tfm' manual output for up to version 4.1.0 and the on-line 
manual on URL: http://emboss.sourceforge.net/docs/adminguide/admin.html ).

GM


From ajb at ebi.ac.uk  Wed Jul 18 06:03:44 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 18 Jul 2007 11:03:44 +0100 (BST)
Subject: [EMBOSS] Database too lare for dbifasta
In-Reply-To: <469DDDB8.5080005@biotek.uio.no>
References: <000001c7c8bb$392f28e0$34572b81@0093Ravi>
	<54178.81.98.241.17.1184744724.squirrel@webmail.ebi.ac.uk>
	<469DDDB8.5080005@biotek.uio.no>
Message-ID: <48767.81.98.241.17.1184753024.squirrel@webmail.ebi.ac.uk>


> Is it possible to highlight this in the EMBOSS manuals somehow?

I've copied this request on to the rest of the developers on
the emboss-bug list.

In answer to a previous question wrt UINT_MAX. That would, of course,
have been possible but the new indexing software had already been
written by then (or, at least, was well advanced) so it wasn't deemed
to be a high priority.

HTH

Alan



From rvijayasatya at ncifcrf.gov  Wed Jul 18 09:37:45 2007
From: rvijayasatya at ncifcrf.gov (Ravi Vijaya Satya)
Date: Wed, 18 Jul 2007 09:37:45 -0400
Subject: [EMBOSS] Database too lare for dbifasta
In-Reply-To: <48767.81.98.241.17.1184753024.squirrel@webmail.ebi.ac.uk>
References: <000001c7c8bb$392f28e0$34572b81@0093Ravi><54178.81.98.241.17.1184744724.squirrel@webmail.ebi.ac.uk><469DDDB8.5080005@biotek.uio.no>
	<48767.81.98.241.17.1184753024.squirrel@webmail.ebi.ac.uk>
Message-ID: <000001c7c940$d2e659b0$34572b81@0093Ravi>

 Thanks for all the information. 

Are there any limits on individual file size in dbxfasta? 

Thanks,
Ravi

-----Original Message-----
From: emboss-bounces at lists.open-bio.org
[mailto:emboss-bounces at lists.open-bio.org] On Behalf Of ajb at ebi.ac.uk
Sent: Wednesday, July 18, 2007 6:04 AM
To: emboss at emboss.open-bio.org
Subject: Re: [EMBOSS] Database too lare for dbifasta


> Is it possible to highlight this in the EMBOSS manuals somehow?

I've copied this request on to the rest of the developers on the emboss-bug
list.

In answer to a previous question wrt UINT_MAX. That would, of course, have
been possible but the new indexing software had already been written by then
(or, at least, was well advanced) so it wasn't deemed to be a high priority.

HTH

Alan


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


From ajb at ebi.ac.uk  Wed Jul 18 10:25:11 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 18 Jul 2007 15:25:11 +0100 (BST)
Subject: [EMBOSS] Database too lare for dbifasta
In-Reply-To: <000001c7c940$d2e659b0$34572b81@0093Ravi>
References: <000001c7c8bb$392f28e0$34572b81@0093Ravi><54178.81.98.241.17.1184744724.squirrel@webmail.ebi.ac.uk><469DDDB8.5080005@biotek.uio.no>
	<48767.81.98.241.17.1184753024.squirrel@webmail.ebi.ac.uk>
	<000001c7c940$d2e659b0$34572b81@0093Ravi>
Message-ID: <42904.81.98.241.17.1184768711.squirrel@webmail.ebi.ac.uk>


> Are there any limits on individual file size in dbxfasta?

64 bits for the dbx* applications rather than 32 bits for the dbi* ones
(give or take a single bit for sign as has already been mentioned).

Alan



From nycademon at spiralrealm.com  Wed Jul 18 13:32:20 2007
From: nycademon at spiralrealm.com (Guido N. Vacano)
Date: Wed, 18 Jul 2007 11:32:20 -0600
Subject: [EMBOSS] JASPAR
Message-ID: <469E4EA4.6000600@spiralrealm.com>

Hello--

    What would be involved in using the JASPAR database
(http://jaspar.genereg.net/) with EMBOSS? The TRANSFAC database is not
available for download (not without paying a hefty fee anyway), which
limits the utility of the tfscan program.

Thanks,
Guido Vacano

From ajb at ebi.ac.uk  Wed Jul 18 15:42:57 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 18 Jul 2007 20:42:57 +0100 (BST)
Subject: [EMBOSS] JASPAR
In-Reply-To: <469E4EA4.6000600@spiralrealm.com>
References: <469E4EA4.6000600@spiralrealm.com>
Message-ID: <35912.81.98.241.17.1184787777.squirrel@webmail.ebi.ac.uk>

Dear Guido,

Very little work from the look of it. The same technique is already
used on the protein side by the 'profit' program so it should be a
simple adaptation.

It looks like a good candidate for 5.1.0

HTH

Alan


> Hello--
>
>     What would be involved in using the JASPAR database
> (http://jaspar.genereg.net/) with EMBOSS? The TRANSFAC database is not
> available for download (not without paying a hefty fee anyway), which
> limits the utility of the tfscan program.
>
> Thanks,
> Guido Vacano
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



From Richard.Rothery at ualberta.ca  Wed Jul 18 15:41:58 2007
From: Richard.Rothery at ualberta.ca (Richard Rothery)
Date: Wed, 18 Jul 2007 13:41:58 -0600
Subject: [EMBOSS] Extracting sequences from PDB files.....
In-Reply-To: <469E4EA4.6000600@spiralrealm.com>
Message-ID: <000301c7c973$b4858620$5e068081@Nordegg>

I would like to extract a primary sequence from a local "new" pdb file
that is a model based on a swissprot/uniprot sequence. I would like to
be able to assess the completeness of the model. Is there an EMBOSS
program that will do this?

Thanks,

Richard Rothery

###############################################
CIHR Molecular Biology of Membrane Proteins Group,
Department of Biochemistry, University of Alberta,
Edmonton T6G 2H7
Ph. (780) 492-2229 Fax. (780) 492-0886
###############################################


-----Original Message-----
From: emboss-bounces at lists.open-bio.org
[mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Guido N. Vacano
Sent: Wednesday, July 18, 2007 11:32 AM
To: EMBOSS Mailing List
Subject: [EMBOSS] JASPAR

Hello--

    What would be involved in using the JASPAR database
(http://jaspar.genereg.net/) with EMBOSS? The TRANSFAC database is not
available for download (not without paying a hefty fee anyway), which
limits the utility of the tfscan program.

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


From dksamuel at gmail.com  Thu Jul 19 00:11:25 2007
From: dksamuel at gmail.com (Duleep Samuel)
Date: Thu, 19 Jul 2007 09:41:25 +0530
Subject: [EMBOSS] JASPAR
In-Reply-To: <35912.81.98.241.17.1184787777.squirrel@webmail.ebi.ac.uk>
References: <469E4EA4.6000600@spiralrealm.com>
	<35912.81.98.241.17.1184787777.squirrel@webmail.ebi.ac.uk>
Message-ID: <a0bf33d50707182111u2d5a79a0qbb6000d62d2349b0@mail.gmail.com>

Sir, Please can mEMBOSS 5.10 be made to read and write pdb files, and play /
convert the the NCBI Cn3d to avi (It helps to understand structures easily)
thanks Samuel

On 7/19/07, ajb at ebi.ac.uk <ajb at ebi.ac.uk> wrote:
>
> Dear Guido,
>
> Very little work from the look of it. The same technique is already
> used on the protein side by the 'profit' program so it should be a
> simple adaptation.
>
> It looks like a good candidate for 5.1.0
>
> HTH
>
> Alan
>
>
> > Hello--
> >
> >     What would be involved in using the JASPAR database
> > (http://jaspar.genereg.net/) with EMBOSS? The TRANSFAC database is not
> > available for download (not without paying a hefty fee anyway), which
> > limits the utility of the tfscan program.
> >
> > Thanks,
> > Guido Vacano
> > _______________________________________________
> > 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 yogi.sundaravadanam at agrf.org.au  Thu Jul 19 01:20:02 2007
From: yogi.sundaravadanam at agrf.org.au (Yogi Sundaravadanam)
Date: Thu, 19 Jul 2007 15:20:02 +1000
Subject: [EMBOSS] Sixpack
In-Reply-To: <469B8E2A.50103@id.unizh.ch>
Message-ID: <H0000294002c3013.1184822401.mailmaster.agrf.org.au@MHS>


Hello all

Does anyone know if the sixpack in the new version of EMBOSS has an option for alternate translation (just like transeq -alternative)? 

Thanks heaps
Yogi
 
 



From REBA at hadassah.org.il  Thu Jul 19 02:55:42 2007
From: REBA at hadassah.org.il (??????? ???? - CONDIOTTI REBA)
Date: Thu, 19 Jul 2007 08:55:42 +0200
Subject: [EMBOSS] meme and mast
Message-ID: <9382027D01ABA04C92708FF63D4EFB2103D4419F@EXCHANGE.DOM.HADASSAH.ORG.IL>

I have two groups of DNA sequences. I want to look for consensus sequences in the first group with meme (which I have been able to do) and then look for that consensus sequence in the second group using mast. I have not been able to find the right command line to do this. 
Any help will be much appreciated.
Reba
 
Reba Condiotti
Goldyne Savad Institute of Gene Therapy
Hadassah University Hospital
POB 12000
Jerusalem 91120 Israel
Tel: 972-2-677-7927
FAX: 972-2-643-0982 






************************************************************************************
This footnote confirms that this email message has been scanned by
PineApp Mail-SeCure for the presence of malicious code, vandals & computer viruses.
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From pmr at ebi.ac.uk  Thu Jul 19 02:47:28 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Thu, 19 Jul 2007 07:47:28 +0100
Subject: [EMBOSS] Database too lare for dbifasta
In-Reply-To: <469DBFF0.3020608@biotek.uio.no>
References: <000001c7c8bb$392f28e0$34572b81@0093Ravi>
	<469DBFF0.3020608@biotek.uio.no>
Message-ID: <469F0900.4050807@ebi.ac.uk>

George Magklaras wrote:

> Question to the developers:
> 
> Why INT_MAX (signed)? Why not unsigned UINT_MAX (to raise it a bit) or 
> another raised limit? It is a bit of an overhead to have to go through 
> the file split stage.

The index file format was originally defined that way by the Staden 
package, and also used by EMBL/EBI CD-ROM indexing and by utilities at 
the Sanger Centre/Institute.

The dbi* index files have two problems - they cannot store file 
positions larger than 2Gb aqnd they do not allow duplicate primary 
identifiers.

We may remove them in a future release - but for smaller databases many 
users seem to find them useful still.

regards,

Peter

From niels at genomics.dk  Fri Jul 20 18:21:55 2007
From: niels at genomics.dk (Niels Larsen)
Date: Sat, 21 Jul 2007 00:21:55 +0200
Subject: [EMBOSS] EMBOSS 5.0
In-Reply-To: <35912.81.98.241.17.1184787777.squirrel@webmail.ebi.ac.uk>
References: <469E4EA4.6000600@spiralrealm.com>
	<35912.81.98.241.17.1184787777.squirrel@webmail.ebi.ac.uk>
Message-ID: <46A13583.4060708@genomics.dk>

Thank you for v5.0 (I have compile-ok on Mandriva Linux 2005 and
Ubuntu Linux 6.06 server version.)

Below are my observations from trying install EMBL locally; I did
it my own way in the end, so maybe not so useful for this list. I
do not need very fast entry access, just a local cache that avoids
request-flooding EBI/NCBI for entries and reduces network traffic.

First I tried dbxflat. It works fine, but indexing takes time; I
estimated a weeks run-time to index the release, and close to a
day for the daily updates on the average (the planned incremental
indexing will help). This means there has to be a machine dedicated
to keep EMBL up to date, because it is cpu-bound. Not unreasonable,
but I wanted to have it work on a cheapo external harddrive, say,
and for it to be ready sooner.

Then I tried BioPerl. It looked like 3 weeks for that run to finish,
so not workable. I have not looked how many entries change between
releases, but having the new release built soon after its available
must be good.

Then I tried to put each record in directories derived from their
accession number: AACI02000001 would be put in AACI/0200, AX101010
in AX1/010, and so on. Each directory has a two column table
(LOOKUP_LIST) with lines like these,

AACI02000001.1  1
AACI02000002.1  1
AACI02000003.1  1
AACI02000004.1  2
AACI02000005.1  2
AACI02000006.1  2
AACI02000007.1  2

where column 1 is the versioned accession number and the second is
the file name that contains its corresponding entry. The entry
files are gzip-compressed and named 1.gz, 2.gz, etc. The release
files stay compressed and are deleted after splitting, so the total
extra space required does not exceed 20% or so of the distribution
size. Creation time is about 26 hours and a typical daily-file is
2-4 minutes; download and import can run in parallel (not done by
threads of course, but by launching the script twice). I tried to
make a balance between disk and ram by caching file handles etc,
but ram does not exceed 330 mb at any time (and stays much lower
most of the time). To access a record, I do "zcat $file | seqret
..... " which is then parsed by bioperl. The access time varies
between 0.03 seconds to 0.3 seconds depending on size, time since
last access, speed of the disk, compression ratio and logic,
humidity outside etc.

Well, I may again have redone something, but at least it filled my
little need. I dont know if others have had the same, or if it is
a feature that EMBOSS should have.

Niels L

PS - one of my mistakes was to get a big slow USB-2 drive under
Linux. The drive is ok, but the ext3 file system broke completely.
I was advised to use firewire or ATA/SATA instead, which allows
health-monitoring with smartctl et al as well (USB does not).

From charles-listes-emboss at plessy.org  Sun Jul 22 06:55:17 2007
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Sun, 22 Jul 2007 19:55:17 +0900
Subject: [EMBOSS] EMBOSS 5.0.0 available as a Debian package.
In-Reply-To: <54666.81.98.241.17.1184486717.squirrel@webmail.ebi.ac.uk>
References: <54666.81.98.241.17.1184486717.squirrel@webmail.ebi.ac.uk>
Message-ID: <20070722105517.GC21806@kunpuu.plessy.org>

Le Sun, Jul 15, 2007 at 09:05:17AM +0100, ajb at ebi.ac.uk a ?crit :
> 1) UNIX
> 
> EMBOSS 5.0.0 for UNIXen is now available from the usual ftp server i.e.
> 
>        ftp://emboss.open-bio.org/pub/EMBOSS/

Dear all,

I am very happy to announce that since this release 5.0.0, the
Debian-Med project provides binary packages for EMBOSS.

Installation on Debian is now as easy as "aptitude install emboss".  By
default, Debian's tool "aptitude" will also install dialign and primer3,
so that the wrappers can work out of the box[1]. For clustalw, due to
licence issues, you will need to add the "non-free" category to your
package list, and "aptitude install clustalw"

Debian's package for EMBOSS has been tested as an experimental package
for version 4.1.0 and is expected to be stable. However, it still has
the following limitations:
 - Since the pcre_internal.h header is not shipped in the "emboss-libs"
   package, compiling external apps will be difficult (but we are
   working on this).
 - EMBASSY is not yet available.
 - Java support is disabled by default.
 - The "cons" and "pscan" had to be renamed "em_cons" and "em_pscan"
   because other programs with this name are already in Debian. However,
   we provide an additional path, /usr/lib/emboss, in which we guarantee
   that names will always be unchanged.

Debian packages for EMBOSS provide a manpage for each program. They are
autobuilt from the acd files, and their informational content is a bit
higher than the --help option, and lower than the tfm manual.

In addition to EMBOSS, we also packaged the emboss-explorer frontend.
Just "apt-get install emboss-explorer" and enjoy it at:
http://localhost/emboss-explorer

We are now working on packaging the EMBASSY programs.

Have a nice day,

Charles Plessy, for the Debian-Med packaging team.

[1] After writing this email, I realised that edialign dissapeared in
    EMBOSS 5.0.0. An updated package will be uploaded, which does not
    depend on dialign.

-- 
Charles Plessy
Debian-Med packaging team
Wako, Saitama, Japan

From sbassi at gmail.com  Sun Jul 22 14:53:22 2007
From: sbassi at gmail.com (Sebastian Bassi)
Date: Sun, 22 Jul 2007 15:53:22 -0300
Subject: [EMBOSS] EMBOSS 5.0.0 available as a Debian package.
In-Reply-To: <20070722105517.GC21806@kunpuu.plessy.org>
References: <54666.81.98.241.17.1184486717.squirrel@webmail.ebi.ac.uk>
	<20070722105517.GC21806@kunpuu.plessy.org>
Message-ID: <b43bf2080707221153i55357922qd02df3a7f0b6c464@mail.gmail.com>

On 7/22/07, Charles Plessy <charles-listes-emboss at plessy.org> wrote:
> I am very happy to announce that since this release 5.0.0, the
> Debian-Med project provides binary packages for EMBOSS.

This is a very nice news!!.
This package works also on Ubuntu?
Best,
SB.

-- 
Bioinformatics news: http://www.bioinformatica.info
Lriser: http://www.linspire.com/lraiser_success.php?serial=318

From charles-listes-emboss at plessy.org  Sun Jul 22 20:33:21 2007
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Mon, 23 Jul 2007 09:33:21 +0900
Subject: [EMBOSS] EMBOSS 5.0.0 available as a Debian package.
In-Reply-To: <b43bf2080707221153i55357922qd02df3a7f0b6c464@mail.gmail.com>
References: <54666.81.98.241.17.1184486717.squirrel@webmail.ebi.ac.uk>
	<20070722105517.GC21806@kunpuu.plessy.org>
	<b43bf2080707221153i55357922qd02df3a7f0b6c464@mail.gmail.com>
Message-ID: <20070723003321.GA10302@kunpuu.plessy.org>

Le Sun, Jul 22, 2007 at 03:53:22PM -0300, Sebastian Bassi a ?crit :
> On 7/22/07, Charles Plessy <charles-listes-emboss at plessy.org> wrote:
> > I am very happy to announce that since this release 5.0.0, the
> > Debian-Med project provides binary packages for EMBOSS.
> 
> This is a very nice news!!.
> This package works also on Ubuntu?

I do not know : I have no Ubuntu to test the binary packages. However,
the source package should be able to produce Ubuntu binary packages
without problems. (Same for Linspire, as you seem to be interested in).

If you are not in a hurry, maybe the easiest way to get emboss in Ubuntu
would be to request it to the MOTU science. Here is a mailing list they
read:

http://lists.tauware.de/listinfo/ubuntu-science

Also, there must be for sure a way to use Launchpad, but I do not know
it...

Have a nice day,

-- 
Charles

From golharam at umdnj.edu  Mon Jul 23 10:56:54 2007
From: golharam at umdnj.edu (Ryan Golhar)
Date: Mon, 23 Jul 2007 10:56:54 -0400
Subject: [EMBOSS] New mEMBOSS on ftp server
In-Reply-To: <41376.81.98.241.17.1184583384.squirrel@webmail.ebi.ac.uk>
Message-ID: <005501c7cd39$b5728640$2d01a8c0@PICO>

What is mEMBOSS?  I'm not familiar with this one and do not see if on the
website

-----Original Message-----
From: emboss-bounces at lists.open-bio.org
[mailto:emboss-bounces at lists.open-bio.org] On Behalf Of ajb at ebi.ac.uk
Sent: Monday, July 16, 2007 6:56 AM
To: emboss-announce at emboss.open-bio.org
Cc: emboss at emboss.open-bio.org
Subject: [EMBOSS] New mEMBOSS on ftp server


A new version of mEMBOSS-5.0.0-setup.exe has been put on the ftp server
(filename unchanged as it is just an enhancement).

It had been noticed that the original version only worked if your Java was
up-to-date (1.6 u2). This new version should also work with Java 1.4 and
Java 1.5. Furthermore, it will auto-detect the Java location and halt
installation if Java is not found.

Alan


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



From golharam at umdnj.edu  Mon Jul 23 11:56:43 2007
From: golharam at umdnj.edu (Ryan Golhar)
Date: Mon, 23 Jul 2007 11:56:43 -0400
Subject: [EMBOSS] EMBOSS 5.0.0 RPMs available
In-Reply-To: <55352.81.98.241.17.1184486754.squirrel@webmail.ebi.ac.uk>
Message-ID: <005a01c7cd42$132efa90$2d01a8c0@PICO>

RPMs for EMBOSS 5.0.0 and the EMBASSY suite are now available at
http://informatics.umdnj.edu/BioRPMs/



-----Original Message-----
From: emboss-bounces at lists.open-bio.org
[mailto:emboss-bounces at lists.open-bio.org] On Behalf Of ajb at ebi.ac.uk
Sent: Sunday, July 15, 2007 4:06 AM
To: emboss at emboss.open-bio.org
Subject: [EMBOSS] EMBOSS 5.0.0 released


1) UNIX

EMBOSS 5.0.0 for UNIXen is now available from the usual ftp server i.e.

       ftp://emboss.open-bio.org/pub/EMBOSS/

as the file EMBOSS-5.0.0.tar.gz . The EMBASSY packages are available in the
same directory. Remember that EMBASSY packages are tailored for each major
release of EMBASSY: do not try to reuse versions from previous EMBOSS
releases.

The sourceforge web pages will be updated tomorrow to show version 5
applications by default. For now they can be accessed explicitly at:
http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/

2) Windows

The Microsoft Windows version is now called mEMBOSS and installs with a
standalone version of Jemboss as a GUI; command line gurus can still use a
command window of course. You must first install Java from java.sun.com (or
java.com) and the vcredist_x86.exe file from the EMBOSS ftp server or the
Microsoft web site (N.B. the latter file is a new version with the current
release, previous releases from the ftp server will not work). mEMBOSS and
vcredist_x86.exe are available in:

       ftp://emboss.open-bio.org/pub/EMBOSS/windows/

Please use the name mEMBOSS (not EMBOSS or EMBOSSWIN) when asking any
questions about the Windows version on the EMBOSS mailing lists. mEMBOSS has
been developed under XP and tested under XP and VISTA, though it will likely
work under several other Windows versions.

3) Changes
See the ChangeLog file

4) Support libraries

UNIX users who use the optional PNG graphics should check that they have a
GD version 2 library (homepage www.libgd.org) installed. GD v1 libraries
will not work correctly with EMBOSS 5.0.0. EMBOSS now uses both PNG and GIF
routines from the GD library. EMBOSS has been tested using GD versions
2.0.33, 2.0.34 and 2.0.35, though some older version 2 libraries should also
work.


Alan


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



From jmullersman at yahoo.com  Mon Jul 23 14:05:00 2007
From: jmullersman at yahoo.com (Jerry Mullersman)
Date: Mon, 23 Jul 2007 11:05:00 -0700 (PDT)
Subject: [EMBOSS] New mEMBOSS on ftp server
In-Reply-To: <005501c7cd39$b5728640$2d01a8c0@PICO>
Message-ID: <527413.86323.qm@web43138.mail.sp1.yahoo.com>

Ryan,

Per the original announcement of EMBOSS 5.0.0, mEMBOSS is the new designation of the Windows version of EMBOSS; see the announcement excerpt below:


2) Windows

The Microsoft Windows version is now called mEMBOSS and installs with a
standalone version of Jemboss as a GUI; command line gurus can still use a
command window of course. You must first install Java from java.sun.com (or
java.com) and the vcredist_x86.exe file from the EMBOSS ftp server or the
Microsoft web site (N.B. the latter file is a new version with the current
release, previous releases from the ftp server will not work). mEMBOSS and
vcredist_x86.exe are available in:

       ftp://emboss.open-bio.org/pub/EMBOSS/windows/

Please use the name mEMBOSS (not EMBOSS or EMBOSSWIN) when asking any
questions about the Windows version on the EMBOSS mailing lists. mEMBOSS has
been developed under XP and tested under XP and VISTA, though it will likely
work under several other Windows versions.

Cheers,

Jerry Mullersman



Ryan Golhar <golharam at umdnj.edu> wrote: What is mEMBOSS?  I'm not familiar with this one and do not see if on the
website

-----Original Message-----
From: emboss-bounces at lists.open-bio.org
[mailto:emboss-bounces at lists.open-bio.org] On Behalf Of ajb at ebi.ac.uk
Sent: Monday, July 16, 2007 6:56 AM
To: emboss-announce at emboss.open-bio.org
Cc: emboss at emboss.open-bio.org
Subject: [EMBOSS] New mEMBOSS on ftp server


A new version of mEMBOSS-5.0.0-setup.exe has been put on the ftp server
(filename unchanged as it is just an enhancement).

It had been noticed that the original version only worked if your Java was
up-to-date (1.6 u2). This new version should also work with Java 1.4 and
Java 1.5. Furthermore, it will auto-detect the Java location and halt
installation if Java is not found.

Alan


_______________________________________________
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



Jerald E. Mullersman, MD, PhD
Associate Professor
Department of Pathology
East Tennessee State University
PO Box 70568
Johnson City, TN 37614
phone: (423) 439-6210   fax:  (423) 439-8060

From Ethan.Hack at ncl.ac.uk  Tue Jul 24 04:28:01 2007
From: Ethan.Hack at ncl.ac.uk (E. Hack)
Date: Tue, 24 Jul 2007 09:28:01 +0100 (GMT Standard Time)
Subject: [EMBOSS] mEMBOSS: Jemboss and proxy servers
Message-ID: <Pine.WNT.4.64.0707240909410.2028@mach12.campus.ncl.ac.uk>

I have installed the new Windows mEMBOSS.  To use external databases, I 
have to connect to the web via a proxy server.  When running EMBOSS 
programs from a Windows command prompt, I can do this successfully using 
the EMBOSS_PROXY environment variable.  With Jemboss, however, external 
connections to databases give me a "socket connect failed" error 
message, and I can't reach external help files either.

The default setting in my Java Control Panel is "Use browser settings". 
I have tried changing this to "Use proxy server" and I have also tried 
specifying the proxy server from inside Jemboss under Preferences - 
Jemboss - Browser Proxies.  Neither of these methods seems to make any 
difference.

I'd be grateful for any suggestions as to what the problem might be. I 
hope the question is an appropriate use of this mailing list and 
apologise if it isn't.  I suspect the solution may be helpful to others 
too (even it should be obvious...) - I don't think there's anything 
particularly unusual about the way my computer is set up.

Ethan Hack

-- 
Dr Ethan Hack                           | E-mail: Ethan.Hack at ncl.ac.uk
School of Biology and Psychology        | Phone:  +44 191 222 8576
Newcastle University                    | Fax:    +44 191 222 5228
Newcastle upon Tyne  NE1 7RU, UK

From Ethan.Hack at ncl.ac.uk  Tue Jul 24 07:01:51 2007
From: Ethan.Hack at ncl.ac.uk (E. Hack)
Date: Tue, 24 Jul 2007 12:01:51 +0100 (GMT Standard Time)
Subject: [EMBOSS] [Fwd:  mEMBOSS: Jemboss and proxy servers]
In-Reply-To: <C2CB91D9.50B2E%tjc@sanger.ac.uk>
References: <C2CB91D9.50B2E%tjc@sanger.ac.uk>
Message-ID: <Pine.WNT.4.64.0707241152290.1340@mach12.campus.ncl.ac.uk>

Perfect!  Problem solved.  I think it would be worth adding this 
information somewhere conspicuous (for Windows, the README.win file 
would be good, as it has high visibility) - everything else in the 
installation is pretty much automatic.

Thanks very much.

Ethan Hack

On Tue, 24 Jul 2007, you wrote:

> Hi Ethan
>
> Try editing the jemboss.properties file in :
> mEMBOSS\jemboss\jar\resources\jemboss.properties
>
> And add EMBOSS_PROXY to the embossEnvironment entry, see the documentation
> for the jemboss.properties file at:
>
> http://emboss.sourceforge.net/Jemboss/install/properties.html
>
> So try adding a line like this:
>
> embossEnvironment=EMBOSS_PROXY=wwwcache.ncl.ac.uk:8080
>
> Then re-run Jemboss. If this works you should be able to access external
> databases.
>
> To get the jemboss browser working for the help files I think you can just
> edit the properties of the jemboss shortcut on your desktop and add "java
> -DproxyHost= wwwcache.ncl.ac.uk -DproxyPort=8080 -jar ..." to the start of
> the Target: field.
>
> Regards
> Tim
>
>
> On 24/7/07 10:25, "ajb at ebi.ac.uk" <ajb at ebi.ac.uk> wrote:
>
>
>> ---------------------------- Original Message ----------------------------
>> Subject: [EMBOSS] mEMBOSS: Jemboss and proxy servers
>> From:    "E. Hack" <Ethan.Hack at ncl.ac.uk>
>> Date:    Tue, July 24, 2007 9:28 am
>> To:      emboss at lists.open-bio.org
>> --------------------------------------------------------------------------
>>
>> I have installed the new Windows mEMBOSS.  To use external databases, I
>> have to connect to the web via a proxy server.  When running EMBOSS
>> programs from a Windows command prompt, I can do this successfully using
>> the EMBOSS_PROXY environment variable.  With Jemboss, however, external
>> connections to databases give me a "socket connect failed" error
>> message, and I can't reach external help files either.
>>
>> The default setting in my Java Control Panel is "Use browser settings".
>> I have tried changing this to "Use proxy server" and I have also tried
>> specifying the proxy server from inside Jemboss under Preferences -
>> Jemboss - Browser Proxies.  Neither of these methods seems to make any
>> difference.
>>
>> I'd be grateful for any suggestions as to what the problem might be. I
>> hope the question is an appropriate use of this mailing list and
>> apologise if it isn't.  I suspect the solution may be helpful to others
>> too (even it should be obvious...) - I don't think there's anything
>> particularly unusual about the way my computer is set up.
>>
>> Ethan Hack

-- 
Dr Ethan Hack                           | E-mail: Ethan.Hack at ncl.ac.uk
School of Biology and Psychology        | Phone:  +44 191 222 8576
Newcastle University                    | Fax:    +44 191 222 5228
Newcastle upon Tyne  NE1 7RU, UK

From sbassi at gmail.com  Tue Jul 24 13:57:15 2007
From: sbassi at gmail.com (Sebastian Bassi)
Date: Tue, 24 Jul 2007 14:57:15 -0300
Subject: [EMBOSS] Problem making EMBOSS 5 in xubuntu
Message-ID: <b43bf2080707241057v3d6d7bbdy4cda28f15e601dfc@mail.gmail.com>

I tried to compile emboss 5 in Xubuntu and I got several errors. Since
the output is about 30Kb, I uploaded the output here to avoid filling
this list:

http://sbassi.googlepages.com/embosserror

I have compilers installed (by build-essential). Xubuntu uses XFCE as
xwindows windows manager.
Best,
SB.

-- 
Bioinformatics news: http://www.bioinformatica.info
Lriser: http://www.linspire.com/lraiser_success.php?serial=318

From sbassi at gmail.com  Tue Jul 24 14:25:08 2007
From: sbassi at gmail.com (Sebastian Bassi)
Date: Tue, 24 Jul 2007 15:25:08 -0300
Subject: [EMBOSS] Problem making EMBOSS 5 in xubuntu
In-Reply-To: <E1IDOnl-0005Pu-IQ@mendel.bio.caltech.edu>
References: <E1IDOnl-0005Pu-IQ@mendel.bio.caltech.edu>
Message-ID: <b43bf2080707241125y5bc08d62jbd7c939b456bfea5@mail.gmail.com>

On 7/24/07, David Mathog <mathog at caltech.edu> wrote:
> Does your system have Xlib.h?  On many linux distros the include
...
> libx11_6-devel-1.1.1-2.1mdv2007.1
....

Yes, the missing package was libx-dev. I installed and now it is
compiling (didn't finish yet).
Thank you very much,
Best,
SB.

-- 
Bioinformatics news: http://www.bioinformatica.info
Lriser: http://www.linspire.com/lraiser_success.php?serial=318

From mathog at caltech.edu  Tue Jul 24 14:08:05 2007
From: mathog at caltech.edu (David Mathog)
Date: Tue, 24 Jul 2007 11:08:05 -0700
Subject: [EMBOSS] Problem making EMBOSS 5 in xubuntu
Message-ID: <E1IDOnl-0005Pu-IQ@mendel.bio.caltech.edu>



> I tried to compile emboss 5 in Xubuntu and I got several errors. Since
> the output is about 30Kb, I uploaded the output here to avoid filling
> this list:
> 
> http://sbassi.googlepages.com/embosserror
> 
> I have compilers installed (by build-essential). Xubuntu uses XFCE as
> xwindows windows manager.

D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -MT
xwin.lo -MD -MP -MF .deps/xwin.Tpo -c xwin.c  -fPIC -DPIC -o .libs/xwin.o
In file included from xwin.c:34:
plxwd.h:22:22: error: X11/Xlib.h: No such file or directory
plxwd.h:23:23: error: X11/Xutil.h: No such file or directory
plxwd.h:24:28: error: X11/cursorfont.h: No such file or directory
plxwd.h:25:24: error: X11/keysym.h: No such file or directory

Does your system have Xlib.h?  On many linux distros the include
files are in separate packages which are not installed by default.
For instance on Mandriva:

% locate Xlib.h
/usr/include/X11/Xlib.h
% rpm -q --whatprovides /usr/include/X11/Xlib.h
libx11_6-devel-1.1.1-2.1mdv2007.1

If the files are installed you may need to give configure a hint
as to where to find them.  (That would be surprising in this case
though, those are pretty common include files.) 

Regards,

David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

From bush at HMC.Edu  Thu Jul 26 12:44:00 2007
From: bush at HMC.Edu (Eliot Bush)
Date: Thu, 26 Jul 2007 09:44:00 -0700
Subject: [EMBOSS] relative abundance/word bias application
Message-ID: <46A8CF50.3040006@hmc.edu>

hello,

I'm wondering if people have any interest in including in EMBOSS an 
application to calculate the relative abundance/bias of words.

The measure I have in mind is that used by Karlin and others (for 
example in Burge, C. et al. PNAS 1992). It is the frequency of a 
particular word, divided by its expected frequency based on the 
frequencies of all its subwords, including gapped subwords. This gives 
you bias at a particular word size, removing the effects at smaller word 
sizes.

For small word sizes there are formulas which one can use, but as you 
get to larger sizes these get unwieldy. I've been working on some code 
which is able calculate this measure up to 10 or 11 bp words in 
reasonable amounts of time. If there is interest, I would be happy to 
contribute it.

Eliot


From simon.andrews at bbsrc.ac.uk  Fri Jul 27 04:24:19 2007
From: simon.andrews at bbsrc.ac.uk (Simon Andrews)
Date: Fri, 27 Jul 2007 09:24:19 +0100
Subject: [EMBOSS] relative abundance/word bias application
In-Reply-To: <46A8CF50.3040006@hmc.edu>
References: <46A8CF50.3040006@hmc.edu>
Message-ID: <E8429619-AD73-4473-8861-102E340DB67A@bbsrc.ac.uk>


On 26 Jul 2007, at 17:44, Eliot Bush wrote:

> hello,
>
> I'm wondering if people have any interest in including in EMBOSS an
> application to calculate the relative abundance/bias of words.
>
> I've been working on some code
> which is able calculate this measure up to 10 or 11 bp words in
> reasonable amounts of time. If there is interest, I would be happy to
> contribute it.

Yes, I was just discussing doing this kind of analysis yesterday.   
We'd certainly appreciate code in EMBOSS which could do this kind of  
calculation.

Cheers

Simon.


From ajb at ebi.ac.uk  Fri Jul 27 05:02:29 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Fri, 27 Jul 2007 10:02:29 +0100 (BST)
Subject: [EMBOSS] relative abundance/word bias application
In-Reply-To: <E8429619-AD73-4473-8861-102E340DB67A@bbsrc.ac.uk>
References: <46A8CF50.3040006@hmc.edu>
	<E8429619-AD73-4473-8861-102E340DB67A@bbsrc.ac.uk>
Message-ID: <58699.81.98.241.17.1185526949.squirrel@webmail.ebi.ac.uk>


> Yes, I was just discussing doing this kind of analysis yesterday.
> We'd certainly appreciate code in EMBOSS which could do this kind of
> calculation.

And, of course, we're more than happy to receive contributions to
EMBOSS.

Alan



From Perdeep.Mehta at STJUDE.ORG  Fri Jul 27 18:13:27 2007
From: Perdeep.Mehta at STJUDE.ORG (Mehta, Perdeep)
Date: Fri, 27 Jul 2007 17:13:27 -0500
Subject: [EMBOSS] help with Profit
Message-ID: <F2235647AC878D438F09255C39842FBC1BB70439@SJMEMXMB03.stjude.sjcrh.local>

Hi,

I am trying to search swissprot protein database with the "Profit"
program. Somehow after running for a while Profit produces following out
put that has no data in it. Here is the text in the generated output
file.

# PROF scan using Henikoff profile pdz_henikoff.prf
# Scores >= threshold 75 (max score 88.53)
#

Does any one have a clue what's wrong with it?  I checked the
installation of swissprot database it works fine I could fetch a
sequence out with seqret.

Thanks in advance for any help.
perdeep

Hartwell Center for Bioinformatics & Biotechnology
St. Jude Children's Research Hospital
Memphis, TN 38105-2794
Tel: 901-495 3774
http://www.hatwellcenter.org/


From zhangcg at bmi.ac.cn  Mon Jul 30 03:37:45 2007
From: zhangcg at bmi.ac.cn (Chenggang Zhang)
Date: Mon, 30 Jul 2007 15:37:45 +0800
Subject: [EMBOSS] EMBOSS 5.0.0 compilation fails on RedHat ver 9.0 (GD
	error)?
Message-ID: <200707301537437988523@bmi.ac.cn>

Dear EMBOSS maintainer,

I have the similary question as Christian reported below. However, even if I have updated the GD to version 2.0.28 or 2.0.35, I still failed to install the EMBOSS5 in my computer (uname information: Linux 2.4.20-8smp #1 SMP Thu Mar 13 17:45:54 EST 2003 i686 i686 i386 GNU/Linux, RedHat ver 9.0). The error information was attached below. Could you please tell me how to solve this question?

make[2]: Entering directory `/dev/shm/EMBOSS-5.0.0/emboss' 
/bin/sh ../libtool --tag=CC   --mode=link gcc  -O2   -o aaindexextract 
aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la 
../ajax/libajax.la ../plplot/libeplplot.la -L/usr/X11R6/lib -lX11  -lm  -lgd 
-lpng -lz -lm 
gcc -O2 -o .libs/aaindexextract aaindexextract.o ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so ../ajax/.libs/libajax.so ../plplot/.libs/libeplplot.so -L/usr/X11R6/lib -lX11 -lgd -lpng -lz -lm  -Wl,--rpath -Wl,/usr/local/emboss5/lib 
../plplot/.libs/libeplplot.so: undefined reference to `gdImageGifPtr' 
../plplot/.libs/libeplplot.so: undefined reference to `gdImageSetThickness' 
../plplot/.libs/libeplplot.so: undefined reference to `gdImagePngPtrEx' 
../plplot/.libs/libeplplot.so: undefined reference to `gdImageCreateTrueColor' 
../plplot/.libs/libeplplot.so: undefined reference to `gdImageSetAntiAliased' 
collect2: ld returned 1 exit status 
make[2]: *** [aaindexextract] Error 1 
make[2]: Leaving directory `/dev/shm/EMBOSS-5.0.0/emboss' 
make[1]: *** [all-recursive] Error 1 
make[1]: Leaving directory `/dev/shm/EMBOSS-5.0.0/emboss' 
make: *** [all-recursive] Error 1 

Best regards,

Sincerely yours,
Chenggang Zhang
2007.07.30 15:36:41

==============================================
Chenggang Zhang, PhD, Professor and Director
Department of Neurobiology
Beijing Institute of Radiation Medicine
Taiping Road 27, Beijing, 100850, China.
Tel: +8610-66931590. Fax: +8610-68169574
Cell phone: +8610-13910133213
Email: zhangcg at bmi.ac.cn,  zcgweb at 126.com
       zcgweb at gmail.com, zcgweb at yahoo.com
==============================================


>================================================================================================================
[EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif support
ajb at ebi.ac.uk ajb at ebi.ac.uk 
Mon Jul 16 12:23:47 EDT 2007 

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Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] 

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

Dear Christian,

Support for GIF was restored in gd 2.0.28 on July 21st, 2004. So, as
mentioned in the announcement, just install an up-to-date gd2 on SLES 9
and the compilation will work.

I've updated the development version of README to reflect this.

Alan



> Dear EMBOSS maintainer
>
> Compilation of EMBOSS 5.0.0 on SLES9 (with all graphical devel libs)
> fails, while linking:
>
> gcc -O2 -D__amd64__ -o .libs/aaindexextract aaindexextract.o
> ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so
> ../ajax/.libs/libajax.so ../plplot/.libs/libeplplot.so -L/usr/X11R6/lib64
> /usr/lib64/libgd.so -L/usr/lib64 -lXpm -lX11
> /usr/lib64/libjpeg.so /usr/lib64/libfreetype.so -lpng12 -lpng -lz -lm
> -Wl,--rpath -Wl,/usr/local/emboss5/lib
>
> ../plplot/.libs/libeplplot.so: undefined reference to `gdImageGifPtr'
>
> Configuration:
> ./configure --prefix=/usr/local/emboss5
>
> It seems for me that EMBOSS 5.0.0 is looking for GIF support despite of
> the fact that newer Versions of
> gd don't support gif anymore (cf. README line 65).
>
> Is there any workarround for the problem (I don't bother changing code)?
>
> Best regards
> Christian
> --
> =============================================================================
> Christian Bolliger
> IT Services                      | http://www.id.uzh.ch/
> Central Systems / HPC   	 | http://www.matterhorn.uzh.ch/
> University of  Zuerich           | E-Mail: christian.bolliger at id.uzh.ch
> Winterthurerstr. 190             | Tel: +41 (0)1 63 56775
> CH-8057 Zuerich; Switzerland     | Fax: +41 (0)1 63 54505
> Mime/S CA:                https://www.ca.unizh.ch/client/
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>




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


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From ajb at ebi.ac.uk  Mon Jul 30 04:22:53 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Mon, 30 Jul 2007 09:22:53 +0100 (BST)
Subject: [EMBOSS] EMBOSS 5.0.0 compilation fails on RedHat ver 9.0 (GD
 error)?
In-Reply-To: <200707301537437988523@bmi.ac.cn>
References: <200707301537437988523@bmi.ac.cn>
Message-ID: <37079.81.98.241.17.1185783773.squirrel@webmail.ebi.ac.uk>

Dear Chenggang Zhang,

There is insufficient detail in your message to be able to answer
it definitively, except to say that it is a GD error. In general:

1) If the GD update is from RPMs that put the gd and gd-devel
   files in the standard RH9 system area (unlikely I suppose as
   RH9 is so old) then you should just do a 'make clean' and
   './configure' EMBOSS again.

2) If you've compiled gd yourself and the libraries are
   in (e.g.) /usr/local/lib and the headers under /usr/local/include
   then, again, 'make clean' but this time add the
      --with-pngdriver=/usr/local
   switch to the './configure' line. (Amend /usr/local appropriately
   if you put the gd files elsewhere).

HTH

Alan

> Dear EMBOSS maintainer,
>
> I have the similary question as Christian reported below. However, even if
> I have updated the GD to version 2.0.28 or 2.0.35, I still failed to
> install the EMBOSS5 in my computer (uname information: Linux 2.4.20-8smp
> #1 SMP Thu Mar 13 17:45:54 EST 2003 i686 i686 i386 GNU/Linux, RedHat ver
> 9.0). The error information was attached below. Could you please tell me
> how to solve this question?
>
> make[2]: Entering directory `/dev/shm/EMBOSS-5.0.0/emboss'
> /bin/sh ../libtool --tag=CC   --mode=link gcc  -O2   -o aaindexextract
> aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la
> ../ajax/libajax.la ../plplot/libeplplot.la -L/usr/X11R6/lib -lX11  -lm
> -lgd
> -lpng -lz -lm
> gcc -O2 -o .libs/aaindexextract aaindexextract.o
> ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so
> ../ajax/.libs/libajax.so ../plplot/.libs/libeplplot.so -L/usr/X11R6/lib
> -lX11 -lgd -lpng -lz -lm  -Wl,--rpath -Wl,/usr/local/emboss5/lib
> ../plplot/.libs/libeplplot.so: undefined reference to `gdImageGifPtr'
> ../plplot/.libs/libeplplot.so: undefined reference to
> `gdImageSetThickness'
> ../plplot/.libs/libeplplot.so: undefined reference to `gdImagePngPtrEx'
> ../plplot/.libs/libeplplot.so: undefined reference to
> `gdImageCreateTrueColor'
> ../plplot/.libs/libeplplot.so: undefined reference to
> `gdImageSetAntiAliased'
> collect2: ld returned 1 exit status
> make[2]: *** [aaindexextract] Error 1
> make[2]: Leaving directory `/dev/shm/EMBOSS-5.0.0/emboss'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/dev/shm/EMBOSS-5.0.0/emboss'
> make: *** [all-recursive] Error 1
>
> Best regards,
>
> Sincerely yours,
> Chenggang Zhang
> 2007.07.30 15:36:41
>
> ==============================================
> Chenggang Zhang, PhD, Professor and Director
> Department of Neurobiology
> Beijing Institute of Radiation Medicine
> Taiping Road 27, Beijing, 100850, China.
> Tel: +8610-66931590. Fax: +8610-68169574
> Cell phone: +8610-13910133213
> Email: zhangcg at bmi.ac.cn,  zcgweb at 126.com
>        zcgweb at gmail.com, zcgweb at yahoo.com
> ==============================================
>
>
>>================================================================================================================
> [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif support
> ajb at ebi.ac.uk ajb at ebi.ac.uk
> Mon Jul 16 12:23:47 EDT 2007
>
> Previous message: [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif
> support
> Next message: [EMBOSS] Sixpack
> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>
> --------------------------------------------------------------------------------
>
> Dear Christian,
>
> Support for GIF was restored in gd 2.0.28 on July 21st, 2004. So, as
> mentioned in the announcement, just install an up-to-date gd2 on SLES 9
> and the compilation will work.
>
> I've updated the development version of README to reflect this.
>
> Alan
>
>
>
>> Dear EMBOSS maintainer
>>
>> Compilation of EMBOSS 5.0.0 on SLES9 (with all graphical devel libs)
>> fails, while linking:
>>
>> gcc -O2 -D__amd64__ -o .libs/aaindexextract aaindexextract.o
>> ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so
>> ../ajax/.libs/libajax.so ../plplot/.libs/libeplplot.so
>> -L/usr/X11R6/lib64
>> /usr/lib64/libgd.so -L/usr/lib64 -lXpm -lX11
>> /usr/lib64/libjpeg.so /usr/lib64/libfreetype.so -lpng12 -lpng -lz -lm
>> -Wl,--rpath -Wl,/usr/local/emboss5/lib
>>
>> ../plplot/.libs/libeplplot.so: undefined reference to `gdImageGifPtr'
>>
>> Configuration:
>> ./configure --prefix=/usr/local/emboss5
>>
>> It seems for me that EMBOSS 5.0.0 is looking for GIF support despite of
>> the fact that newer Versions of
>> gd don't support gif anymore (cf. README line 65).
>>
>> Is there any workarround for the problem (I don't bother changing code)?
>>
>> Best regards
>> Christian
>> --
>> =============================================================================
>> Christian Bolliger
>> IT Services                      | http://www.id.uzh.ch/
>> Central Systems / HPC   	 | http://www.matterhorn.uzh.ch/
>> University of  Zuerich           | E-Mail: christian.bolliger at
>> id.uzh.ch
>> Winterthurerstr. 190             | Tel: +41 (0)1 63 56775
>> CH-8057 Zuerich; Switzerland     | Fax: +41 (0)1 63 54505
>> Mime/S CA:                https://www.ca.unizh.ch/client/
>>
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>
>
>
>
> --------------------------------------------------------------------------------
>
>
> Previous message: [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif
> support
> Next message: [EMBOSS] Sixpack
> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>
> --------------------------------------------------------------------------------
> More information about the EMBOSS mailing list
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



From zhangcg at bmi.ac.cn  Mon Jul 30 08:07:15 2007
From: zhangcg at bmi.ac.cn (Chenggang Zhang)
Date: Mon, 30 Jul 2007 20:07:15 +0800
Subject: [EMBOSS] EMBOSS 5.0.0 compilation fails on RedHat ver 9.0
	(GDerror)?
References: <200707301537437988523@bmi.ac.cn>,
	<37079.81.98.241.17.1185783773.squirrel@webmail.ebi.ac.uk>
Message-ID: <200707302007137492344@bmi.ac.cn>

Dear Dr. Aln,

Thank you for the kind suggestion. The installation is now OK using the following command:
'./configure --with-pngdriver=/usr/local'

Best regards,

Sincerely yours,
Chenggang Zhang
2007-07-30 20:06:16

==============================================
Chenggang Zhang, PhD, Professor and Director
Department of Neurobiology
Beijing Institute of Radiation Medicine
Taiping Road 27, Beijing, 100850, China.
Tel: +8610-66931590. Fax: +8610-68169574
Cell phone: +8610-13910133213
Email: zhangcg at bmi.ac.cn,  zcgweb at 126.com
       zcgweb at yahoo.com, zcgweb at gmail.com
==============================================

=======Your original message at 2007-07-30 16:23:07=======

>Dear Chenggang Zhang,
>
>There is insufficient detail in your message to be able to answer
>it definitively, except to say that it is a GD error. In general:
>
>1) If the GD update is from RPMs that put the gd and gd-devel
>   files in the standard RH9 system area (unlikely I suppose as
>   RH9 is so old) then you should just do a 'make clean' and
>   './configure' EMBOSS again.
>
>2) If you've compiled gd yourself and the libraries are
>   in (e.g.) /usr/local/lib and the headers under /usr/local/include
>   then, again, 'make clean' but this time add the
>      --with-pngdriver=/usr/local
>   switch to the './configure' line. (Amend /usr/local appropriately
>   if you put the gd files elsewhere).
>
>HTH
>
>Alan
>
>> Dear EMBOSS maintainer,
>>
>> I have the similary question as Christian reported below. However, even if
>> I have updated the GD to version 2.0.28 or 2.0.35, I still failed to
>> install the EMBOSS5 in my computer (uname information: Linux 2.4.20-8smp
>> #1 SMP Thu Mar 13 17:45:54 EST 2003 i686 i686 i386 GNU/Linux, RedHat ver
>> 9.0). The error information was attached below. Could you please tell me
>> how to solve this question?
>>
>> make[2]: Entering directory `/dev/shm/EMBOSS-5.0.0/emboss'
>> /bin/sh ../libtool --tag=CC   --mode=link gcc  -O2   -o aaindexextract
>> aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la
>> ../ajax/libajax.la ../plplot/libeplplot.la -L/usr/X11R6/lib -lX11  -lm
>> -lgd
>> -lpng -lz -lm
>> gcc -O2 -o .libs/aaindexextract aaindexextract.o
>> ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so
>> ../ajax/.libs/libajax.so ../plplot/.libs/libeplplot.so -L/usr/X11R6/lib
>> -lX11 -lgd -lpng -lz -lm  -Wl,--rpath -Wl,/usr/local/emboss5/lib
>> ../plplot/.libs/libeplplot.so: undefined reference to `gdImageGifPtr'
>> ../plplot/.libs/libeplplot.so: undefined reference to
>> `gdImageSetThickness'
>> ../plplot/.libs/libeplplot.so: undefined reference to `gdImagePngPtrEx'
>> ../plplot/.libs/libeplplot.so: undefined reference to
>> `gdImageCreateTrueColor'
>> ../plplot/.libs/libeplplot.so: undefined reference to
>> `gdImageSetAntiAliased'
>> collect2: ld returned 1 exit status
>> make[2]: *** [aaindexextract] Error 1
>> make[2]: Leaving directory `/dev/shm/EMBOSS-5.0.0/emboss'
>> make[1]: *** [all-recursive] Error 1
>> make[1]: Leaving directory `/dev/shm/EMBOSS-5.0.0/emboss'
>> make: *** [all-recursive] Error 1
>>
>> Best regards,
>>
>> Sincerely yours,
>> Chenggang Zhang
>> 2007.07.30 15:36:41
>>
>> ==============================================
>> Chenggang Zhang, PhD, Professor and Director
>> Department of Neurobiology
>> Beijing Institute of Radiation Medicine
>> Taiping Road 27, Beijing, 100850, China.
>> Tel: +8610-66931590. Fax: +8610-68169574
>> Cell phone: +8610-13910133213
>> Email: zhangcg at bmi.ac.cn,  zcgweb at 126.com
>>        zcgweb at gmail.com, zcgweb at yahoo.com
>> ==============================================
>>
>>
>>>================================================================================================================
>> [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif support
>> ajb at ebi.ac.uk ajb at ebi.ac.uk
>> Mon Jul 16 12:23:47 EDT 2007
>>
>> Previous message: [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif
>> support
>> Next message: [EMBOSS] Sixpack
>> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>>
>> --------------------------------------------------------------------------------
>>
>> Dear Christian,
>>
>> Support for GIF was restored in gd 2.0.28 on July 21st, 2004. So, as
>> mentioned in the announcement, just install an up-to-date gd2 on SLES 9
>> and the compilation will work.
>>
>> I've updated the development version of README to reflect this.
>>
>> Alan
>>
>>
>>
>>> Dear EMBOSS maintainer
>>>
>>> Compilation of EMBOSS 5.0.0 on SLES9 (with all graphical devel libs)
>>> fails, while linking:
>>>
>>> gcc -O2 -D__amd64__ -o .libs/aaindexextract aaindexextract.o
>>> ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so
>>> ../ajax/.libs/libajax.so ../plplot/.libs/libeplplot.so
>>> -L/usr/X11R6/lib64
>>> /usr/lib64/libgd.so -L/usr/lib64 -lXpm -lX11
>>> /usr/lib64/libjpeg.so /usr/lib64/libfreetype.so -lpng12 -lpng -lz -lm
>>> -Wl,--rpath -Wl,/usr/local/emboss5/lib
>>>
>>> ../plplot/.libs/libeplplot.so: undefined reference to `gdImageGifPtr'
>>>
>>> Configuration:
>>> ./configure --prefix=/usr/local/emboss5
>>>
>>> It seems for me that EMBOSS 5.0.0 is looking for GIF support despite of
>>> the fact that newer Versions of
>>> gd don't support gif anymore (cf. README line 65).
>>>
>>> Is there any workarround for the problem (I don't bother changing code)?
>>>
>>> Best regards
>>> Christian
>>> --
>>> =============================================================================
>>> Christian Bolliger
>>> IT Services                      | http://www.id.uzh.ch/
>>> Central Systems / HPC   	 | http://www.matterhorn.uzh.ch/
>>> University of  Zuerich           | E-Mail: christian.bolliger at
>>> id.uzh.ch
>>> Winterthurerstr. 190             | Tel: +41 (0)1 63 56775
>>> CH-8057 Zuerich; Switzerland     | Fax: +41 (0)1 63 54505
>>> Mime/S CA:                https://www.ca.unizh.ch/client/
>>>
>>> _______________________________________________
>>> EMBOSS mailing list
>>> EMBOSS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>
>>
>>
>>
>>
>> --------------------------------------------------------------------------------
>>
>>
>> Previous message: [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif
>> support
>> Next message: [EMBOSS] Sixpack
>> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>>
>> --------------------------------------------------------------------------------
>> More information about the EMBOSS mailing list
>>
>>
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>
>

= = = = = = = = = = = = = = = = = = = =



From gbottu at vub.ac.be  Fri Jul  6 08:40:46 2007
From: gbottu at vub.ac.be (Guy Bottu)
Date: Fri, 06 Jul 2007 10:40:46 +0200
Subject: [EMBOSS] MRS 3 as EMBOSS sequence access mechanism
Message-ID: <468E000E.5020201@vub.ac.be>

	Dear all,

The MRS servers are shifting from version 2 to version 3. A result is that the 
EMBOSS sequence access mechanism "mrs" does not work anymore. The reason is that 
  the URL to be generated by the software is not anymore something like
http://mrs.cmbi.kun.nl/mrs/cgi-bin/mrs.cgi?db=sprot%2Btrembl&query=id:papa1_carpa&format=entry&exp=1&save_to=text/plain
but
http://mrs.cmbi.kun.nl/mrs-3/plain.do?db=uniprot&id=papa1_carpa
It is not possible to search several databanks at the same time, but MRS 3 has 
composite indexes for e.g. uniprot (=sprot+trembl) or embl (=nonredundant 
release + updates). It is also impossible to make a query with wild cards. A 
suppementary problem is that the MRS WWW server wants to set a cookie.

Do you think the next release of EMBOSS could support MRS 3 (maybe, in the 
tradition of backward compatibility, have both "mrs" and "mrs3" access methods)?

And are some of you really using MRS WWW as access sequence access mechanism for 
EMBOSS ?

	Regards,
	Guy Bottu,
	Belgian EMBnet Node


From pmr at ebi.ac.uk  Fri Jul  6 09:12:30 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 06 Jul 2007 10:12:30 +0100
Subject: [EMBOSS] [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E000E.5020201@vub.ac.be>
References: <468E000E.5020201@vub.ac.be>
Message-ID: <468E077E.5080706@ebi.ac.uk>

Guy Bottu wrote:

> Do you think the next release of EMBOSS could support MRS 3 (maybe, in the 
> tradition of backward compatibility, have both "mrs" and "mrs3" access methods)?

Tricky - today is my last day for making changes before going on vacation until 
the release!

But yes I can do it. Is mrs3 the best name? Probably it is, because the URL now 
contains "mrs-3" :-)

Peter


From pmr at ebi.ac.uk  Fri Jul  6 09:20:47 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 06 Jul 2007 10:20:47 +0100
Subject: [EMBOSS] [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E000E.5020201@vub.ac.be>
References: <468E000E.5020201@vub.ac.be>
Message-ID: <468E096F.70102@ebi.ac.uk>

Guy Bottu wrote:

> It is not possible to search several databanks at the same time, but MRS 3 has 
> composite indexes for e.g. uniprot (=sprot+trembl) or embl (=nonredundant 
> release + updates). It is also impossible to make a query with wild cards. A 
> suppementary problem is that the MRS WWW server wants to set a cookie.

We do not handle cookies. MRS3 will have to work without them. It appears it does.

How does MRS3 search for other fields (accession, etc.)?

Where is the MRS server documentation??? I found no documentation of the URL 
syntax or query fields at the CMBI server.

Peter


From pmr at ebi.ac.uk  Fri Jul  6 09:31:36 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 06 Jul 2007 10:31:36 +0100
Subject: [EMBOSS] [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E000E.5020201@vub.ac.be>
References: <468E000E.5020201@vub.ac.be>
Message-ID: <468E0BF8.4030801@ebi.ac.uk>

Guy Bottu wrote:
> The MRS servers are shifting from version 2 to version 3. A result is that the 
> EMBOSS sequence access mechanism "mrs" does not work anymore. The reason is that 
>   the URL to be generated by the software is not anymore something like
> http://mrs.cmbi.kun.nl/mrs/cgi-bin/mrs.cgi?db=sprot%2Btrembl&query=id:papa1_carpa&format=entry&exp=1&save_to=text/plain
> but
> http://mrs.cmbi.kun.nl/mrs-3/plain.do?db=uniprot&id=papa1_carpa

Hah .. that works from wget but when I try that URL within EMBOSS I get nonsense 
back. The web page returns is a 302 error saying:

The document has moved <a 
href="http://mrs.cmbi.ru.nl/mrs-3/?db=embl&amp;id=x13776Host:">here</a>

with an href of http://mrs.cmbi.ru.nl/mrs-3/?db=embl&amp;id=x13776Host:
(yes, with Host: at the end)


> Do you think the next release of EMBOSS could support MRS 3 (maybe, in the 
> tradition of backward compatibility, have both "mrs" and "mrs3" access methods)?

I will add an MRS3 method. Whether it will work before EMBOSS 5.1.0 is another 
question :-)

Peter


From pmr at ebi.ac.uk  Fri Jul  6 10:13:58 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 06 Jul 2007 11:13:58 +0100
Subject: [EMBOSS] [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E000E.5020201@vub.ac.be>
References: <468E000E.5020201@vub.ac.be>
Message-ID: <468E15E6.1030609@ebi.ac.uk>

Guy Bottu wrote:
> 	Dear all,
> 
> The MRS servers are shifting from version 2 to version 3. A result is that the 
> EMBOSS sequence access mechanism "mrs" does not work anymore. The reason is that 
>   the URL to be generated by the software is not anymore something like
> http://mrs.cmbi.kun.nl/mrs/cgi-bin/mrs.cgi?db=sprot%2Btrembl&query=id:papa1_carpa&format=entry&exp=1&save_to=text/plain
> but
> http://mrs.cmbi.kun.nl/mrs-3/plain.do?db=uniprot&id=papa1_carpa

Hmmm ... I have something working.

The MRS3 server absolutely requires HTTP/1.x on the GET line.

The MRS2 server was happy without it (though I am not sure why it was the only 
EMBOSS method that did not use it)

Peter


From gbottu at vub.ac.be  Mon Jul  9 07:53:25 2007
From: gbottu at vub.ac.be (Guy Bottu)
Date: Mon, 09 Jul 2007 09:53:25 +0200
Subject: [EMBOSS] [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <468E096F.70102@ebi.ac.uk>
References: <468E000E.5020201@vub.ac.be> <468E096F.70102@ebi.ac.uk>
Message-ID: <4691E975.7050500@vub.ac.be>

Peter Rice wrote:
> How does MRS3 search for other fields (accession, etc.)

Alas, with MRS2 you could write a single URL to perform a query and then
retrieve the result as plain text. With MRS3 this has become impossible,
because there are now separate programs. Could EMBOSS eventually first
ask for a query.do, parse the reply and then ask for a plain.do ?
Or you could consider using the Web services instead. I have no 
experience with the Web services under MRS3 ; I will in the coming weeks 
try to get informed.

> Where is the MRS server documentation??? I found no documentation of the URL 
> syntax or query fields at the CMBI server.

There is no documentation for the moment. Well, let's not blame dear 
Maarten, he is alone in his corner with a big development project...

You can however find a list of available databanks, with for each 
databank the available field shortnames. It is possible to write an URL
like ..../mrs-3/query.do?db=uniprot&query=id:papa?_carpa|ac:papa?_carpa

	Guy




From pmr at ebi.ac.uk  Sun Jul  8 14:22:00 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Sun, 08 Jul 2007 15:22:00 +0100
Subject: [EMBOSS] [emboss-dev] MRS 3 as EMBOSS sequence access mechanism
In-Reply-To: <4691E975.7050500@vub.ac.be>
References: <468E000E.5020201@vub.ac.be> <468E096F.70102@ebi.ac.uk>
	<4691E975.7050500@vub.ac.be>
Message-ID: <4690F308.2000108@ebi.ac.uk>

Guy Bottu wrote:
> Alas, with MRS2 you could write a single URL to perform a query and then
> retrieve the result as plain text. With MRS3 this has become impossible,
> because there are now separate programs. Could EMBOSS eventually first
> ask for a query.do, parse the reply and then ask for a plain.do ?
> Or you could consider using the Web services instead. I have no 
> experience with the Web services under MRS3 ; I will in the coming weeks 
> try to get informed.

Yes ... we already do something like that for Entrez.

> There is no documentation for the moment. Well, let's not blame dear 
> Maarten, he is alone in his corner with a big development project...
> 
> You can however find a list of available databanks, with for each 
> databank the available field shortnames. It is possible to write an URL
> like ..../mrs-3/query.do?db=uniprot&query=id:papa?_carpa|ac:papa?_carpa

Thanks. The query access will now have to wait for EMBOSS 5.1.0. The 
basic ID retrieval is in the 5.0.0 release.

regards,

Peter


From charles-listes-emboss at plessy.org  Sun Jul  8 14:02:57 2007
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Sun, 8 Jul 2007 23:02:57 +0900
Subject: [EMBOSS] Antwort:  Manpage generator
In-Reply-To: <OFEA4A36A9.0EB51F74-ONC12571DF.00259DD5-C12571DF.00264720@schering.de>
References: <20060904042850.GC14634@kunpuu.plessy.org>
	<OFEA4A36A9.0EB51F74-ONC12571DF.00259DD5-C12571DF.00264720@schering.de>
Message-ID: <20070708140257.GA5423@kunpuu.plessy.org>

> Charles Plessy schrieb am 04/09/2006 06:28:50:
> > 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).

Le Mon, Sep 04, 2006 at 08:57:54AM +0200, David.Bauer at SCHERING.DE a ?crit :
> 
> 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.

Dear all,

Thanks do David's suggestion, I managed to write a manpage generator for
EMBOSS programs. It uses the EMBOSS::ACD library (which we ship in
Debian in the package libemboss-acd-perl) to create a docbook XML
document, which is transformed into a manpage with the xsltproc program.
The reason why the generator does not directly write the manpage is
simply that I do not know the nroff syntax.

You can download it from the following URI:
http://svn.debian.org/wsvn/pkg-emboss/emboss/trunk/debian/acd2docbook.pl?op=file&rev=0&sc=0

I have put a couple of examples manpages on my personal website in the
following directory:
http://charles.plessy.org/debian/emboss/

I intend to distribute manpages for all emboss programs in the Debian
package which will be updated after the release of EMBOSS 5.0

Have a nice day,

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


From Richard.Rothery at ualberta.ca  Mon Jul  9 22:29:56 2007
From: Richard.Rothery at ualberta.ca (Richard Rothery)
Date: Mon, 9 Jul 2007 16:29:56 -0600
Subject: [EMBOSS] FW: Ebi_blast and Ebi_tmhmm....
Message-ID: <000501c7c278$ad50b480$5e068081@Nordegg>

Hi,

 

I am trying to install the Ebi_blast (
<http://oryx.ulb.ac.be/embosshelp/ebi_blast.html>
http://oryx.ulb.ac.be/embosshelp/ebi_blast.html) and Ebi_tmhmm (
<http://oryx.ulb.ac.be/embosshelp/ebi_tmhmm.html>
http://oryx.ulb.ac.be/embosshelp/ebi_tmhmm.html) programs or add them to
my EMBOSS installation, and have had not success. Are these part of the
latest release? I think I have version 4.1. Are these perl scripts?

 

Thanks!

 

Richard A. Rothery

 

###############################################

CIHR Membrane Protein Research Group,

Department of Biochemistry, University of Alberta,

Edmonton T6G 2H7

Ph. (780) 492-2229 Fax. (780) 492-0886

###############################################

 



From uludag at ebi.ac.uk  Tue Jul 10 09:03:32 2007
From: uludag at ebi.ac.uk (Mahmut Uludag)
Date: Tue, 10 Jul 2007 10:03:32 +0100
Subject: [EMBOSS] FW: Ebi_blast and Ebi_tmhmm....
In-Reply-To: <000501c7c278$ad50b480$5e068081@Nordegg>
References: <000501c7c278$ad50b480$5e068081@Nordegg>
Message-ID: <1184058212.5690.4.camel@emboss2.ebi.ac.uk>


> I am trying to install the Ebi_blast (
> <http://oryx.ulb.ac.be/embosshelp/ebi_blast.html>
> http://oryx.ulb.ac.be/embosshelp/ebi_blast.html) and Ebi_tmhmm (
> <http://oryx.ulb.ac.be/embosshelp/ebi_tmhmm.html>
> http://oryx.ulb.ac.be/embosshelp/ebi_tmhmm.html) programs or add them to
> my EMBOSS installation, and have had not success. Are these part of the
> latest release?

I have searched my EMBOSS-4.1 and EMBOSS-CVS installations for an acd
file for the above applications. Finding no acd files I can say that
they are not standard applications in the latest release.

Regards,
Mahmut




From david.bauer at bayerhealthcare.com  Tue Jul 10 09:11:19 2007
From: david.bauer at bayerhealthcare.com (david.bauer at bayerhealthcare.com)
Date: Tue, 10 Jul 2007 11:11:19 +0200
Subject: [EMBOSS] FW: Ebi_blast and Ebi_tmhmm....
In-Reply-To: <1184058212.5690.4.camel@emboss2.ebi.ac.uk>
Message-ID: <OFAEC01053.7D958CB4-ONC1257314.00325CAA-C1257314.00327A9C@schering.de>

They are part of "wrappers4EMBOSS".
More information you can find at the wemboss site
http://www.wemboss.org/

Cheers,
David.

emboss-bounces at lists.open-bio.org schrieb am 10/07/2007 11:03:32:

> 
> > I am trying to install the Ebi_blast (
> > <http://oryx.ulb.ac.be/embosshelp/ebi_blast.html>
> > http://oryx.ulb.ac.be/embosshelp/ebi_blast.html) and Ebi_tmhmm (
> > <http://oryx.ulb.ac.be/embosshelp/ebi_tmhmm.html>
> > http://oryx.ulb.ac.be/embosshelp/ebi_tmhmm.html) programs or add them 
to
> > my EMBOSS installation, and have had not success. Are these part of 
the
> > latest release?
> 
> I have searched my EMBOSS-4.1 and EMBOSS-CVS installations for an acd
> file for the above applications. Finding no acd files I can say that
> they are not standard applications in the latest release.
> 
> Regards,
> Mahmut
> 
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss



From ajb at ebi.ac.uk  Sun Jul 15 08:05:54 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Sun, 15 Jul 2007 09:05:54 +0100 (BST)
Subject: [EMBOSS] EMBOSS 5.0.0 released
Message-ID: <55352.81.98.241.17.1184486754.squirrel@webmail.ebi.ac.uk>

1) UNIX

EMBOSS 5.0.0 for UNIXen is now available from the usual ftp server i.e.

       ftp://emboss.open-bio.org/pub/EMBOSS/

as the file EMBOSS-5.0.0.tar.gz . The EMBASSY packages are available
in the same directory. Remember that EMBASSY packages are tailored for
each major release of EMBASSY: do not try to reuse versions from
previous EMBOSS releases.

The sourceforge web pages will be updated tomorrow to show version 5
applications by default. For now they can be accessed explicitly at:
http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/

2) Windows

The Microsoft Windows version is now called mEMBOSS and installs with
a standalone version of Jemboss as a GUI; command line gurus can still
use a command window of course. You must first install Java from
java.sun.com (or java.com) and the vcredist_x86.exe file from the
EMBOSS ftp server or the Microsoft web site (N.B. the latter file is a
new version with the current release, previous releases from the ftp
server will not work). mEMBOSS and vcredist_x86.exe are available in:

       ftp://emboss.open-bio.org/pub/EMBOSS/windows/

Please use the name mEMBOSS (not EMBOSS or EMBOSSWIN) when asking any
questions about the Windows version on the EMBOSS mailing lists.
mEMBOSS has been developed under XP and tested under XP and VISTA, though
it will likely work under several other Windows versions.

3) Changes
See the ChangeLog file

4) Support libraries

UNIX users who use the optional PNG graphics should check that they
have a GD version 2 library (homepage www.libgd.org) installed. GD v1
libraries will not work correctly with EMBOSS 5.0.0. EMBOSS now uses
both PNG and GIF routines from the GD library. EMBOSS has been tested
using GD versions 2.0.33, 2.0.34 and 2.0.35, though some older version
2 libraries should also work.


Alan




From ajb at ebi.ac.uk  Mon Jul 16 10:56:24 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Mon, 16 Jul 2007 11:56:24 +0100 (BST)
Subject: [EMBOSS] New mEMBOSS on ftp server
Message-ID: <41376.81.98.241.17.1184583384.squirrel@webmail.ebi.ac.uk>

A new version of mEMBOSS-5.0.0-setup.exe has been put on the
ftp server (filename unchanged as it is just an enhancement).

It had been noticed that the original version only worked if
your Java was up-to-date (1.6 u2). This new version should also
work with Java 1.4 and Java 1.5. Furthermore, it will auto-detect
the Java location and halt installation if Java is not found.

Alan




From christian.bolliger at id.unizh.ch  Mon Jul 16 15:26:34 2007
From: christian.bolliger at id.unizh.ch (Christian Bolliger)
Date: Mon, 16 Jul 2007 17:26:34 +0200
Subject: [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif support
Message-ID: <469B8E2A.50103@id.unizh.ch>

Dear EMBOSS maintainer

Compilation of EMBOSS 5.0.0 on SLES9 (with all graphical devel libs) fails, while linking:

gcc -O2 -D__amd64__ -o .libs/aaindexextract aaindexextract.o  ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so
../ajax/.libs/libajax.so ../plplot/.libs/libeplplot.so -L/usr/X11R6/lib64 /usr/lib64/libgd.so -L/usr/lib64 -lXpm -lX11
/usr/lib64/libjpeg.so /usr/lib64/libfreetype.so -lpng12 -lpng -lz -lm  -Wl,--rpath -Wl,/usr/local/emboss5/lib

../plplot/.libs/libeplplot.so: undefined reference to `gdImageGifPtr'

Configuration:
./configure --prefix=/usr/local/emboss5

It seems for me that EMBOSS 5.0.0 is looking for GIF support despite of the fact that newer Versions of
gd don't support gif anymore (cf. README line 65).

Is there any workarround for the problem (I don't bother changing code)?

Best regards
Christian
-- 
=============================================================================
Christian Bolliger
IT Services                      | http://www.id.uzh.ch/
Central Systems / HPC   	 | http://www.matterhorn.uzh.ch/
University of  Zuerich           | E-Mail: christian.bolliger at id.uzh.ch
Winterthurerstr. 190             | Tel: +41 (0)1 63 56775
CH-8057 Zuerich; Switzerland     | Fax: +41 (0)1 63 54505
Mime/S CA:                https://www.ca.unizh.ch/client/



From ajb at ebi.ac.uk  Mon Jul 16 16:23:47 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Mon, 16 Jul 2007 17:23:47 +0100 (BST)
Subject: [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif support
In-Reply-To: <469B8E2A.50103@id.unizh.ch>
References: <469B8E2A.50103@id.unizh.ch>
Message-ID: <57855.81.98.241.17.1184603027.squirrel@webmail.ebi.ac.uk>

Dear Christian,

Support for GIF was restored in gd 2.0.28 on July 21st, 2004. So, as
mentioned in the announcement, just install an up-to-date gd2 on SLES 9
and the compilation will work.

I've updated the development version of README to reflect this.

Alan



> Dear EMBOSS maintainer
>
> Compilation of EMBOSS 5.0.0 on SLES9 (with all graphical devel libs)
> fails, while linking:
>
> gcc -O2 -D__amd64__ -o .libs/aaindexextract aaindexextract.o
> ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so
> ../ajax/.libs/libajax.so ../plplot/.libs/libeplplot.so -L/usr/X11R6/lib64
> /usr/lib64/libgd.so -L/usr/lib64 -lXpm -lX11
> /usr/lib64/libjpeg.so /usr/lib64/libfreetype.so -lpng12 -lpng -lz -lm
> -Wl,--rpath -Wl,/usr/local/emboss5/lib
>
> ../plplot/.libs/libeplplot.so: undefined reference to `gdImageGifPtr'
>
> Configuration:
> ./configure --prefix=/usr/local/emboss5
>
> It seems for me that EMBOSS 5.0.0 is looking for GIF support despite of
> the fact that newer Versions of
> gd don't support gif anymore (cf. README line 65).
>
> Is there any workarround for the problem (I don't bother changing code)?
>
> Best regards
> Christian
> --
> =============================================================================
> Christian Bolliger
> IT Services                      | http://www.id.uzh.ch/
> Central Systems / HPC   	 | http://www.matterhorn.uzh.ch/
> University of  Zuerich           | E-Mail: christian.bolliger at id.uzh.ch
> Winterthurerstr. 190             | Tel: +41 (0)1 63 56775
> CH-8057 Zuerich; Switzerland     | Fax: +41 (0)1 63 54505
> Mime/S CA:                https://www.ca.unizh.ch/client/
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>




From virtuellefestplatte at gmx.net  Tue Jul 17 05:50:30 2007
From: virtuellefestplatte at gmx.net (Sascha Engel)
Date: Tue, 17 Jul 2007 07:50:30 +0200
Subject: [EMBOSS] Installationproblem emboss-explorer
Message-ID: <20070717055030.195460@gmx.net>

Hi,

I have installed EMBOSS-5.0.0 without any problems and now I try to install emboss-explorer on suse 9.2 (i586).

Unfortunately I get an early error:

Checking if your kit is complete...
Looks good
MakeMaker FATAL: prerequisites not found (Parse::RecDescent 1.9)

        Please install these modules first and rerun 'perl Makefile.PL'.

As far as I know there is no Parse::RecDescent 1.9 - package available for Suse 9.2. I tried to install the fedora package (1.94), but without success.
Anyone went through this before? 

Thanks for helping

Sascha







-- 
Psssst! Schon vom neuen GMX MultiMessenger geh?rt?
Der kanns mit allen: http://www.gmx.net/de/go/multimessenger


From dksamuel at gmail.com  Tue Jul 17 07:16:33 2007
From: dksamuel at gmail.com (Duleep Samuel)
Date: Tue, 17 Jul 2007 12:46:33 +0530
Subject: [EMBOSS] JEMBOSS and mEMBOSS works well on WIN XP Thanks
In-Reply-To: <a0bf33d50707170015y4aeeab5ah2129519a975ffb0c@mail.gmail.com>
References: <a0bf33d50707170009t2819a11ale53403890d73e515@mail.gmail.com>
	<a0bf33d50707170015y4aeeab5ah2129519a975ffb0c@mail.gmail.com>
Message-ID: <a0bf33d50707170016q2d0dd482kd23e3af3d9567027@mail.gmail.com>

Dear all, very happy to have used JEMBOSS and mEMBOSS on WIN XP for 4 hrs
yesterday, real nice program, I remembered the days when I tried to use
EMBOSS GUI with Vigyaan CD, NERC DVD (bootable Knoppix), other GUIs,
miserably failed to load JEMBOSS, and EMBOSS on linux.then EMBOSS 4 on win
XP with its command line, where I typed till my fingers got worn out.
Dreamed of a GUI, Thanks from a grateful user to the great team which made
JEMBOSS and mEMBOSS on WIN XP, with regards Samuel, India.


From scott at cs.wits.ac.za  Tue Jul 17 07:01:42 2007
From: scott at cs.wits.ac.za (Scott Hazelhurst)
Date: Tue, 17 Jul 2007 10:01:42 +0300
Subject: [EMBOSS] EST clustering program
Message-ID: <20070717065805.M59277@cs.wits.ac.za>



One of the applications listed in the suggested list for EMBOSS is a program that does
clustering. We've been working on such a program with collaborators (mainly for ESTs)
and we've recently developed an EMBOSS wrapper for it. Is there any way of making it
available to the community?

Scott


---- Scott Hazelhurst ------------------------  scott at cs.wits.ac.za --------
Bioinformatics & Computer Science, University of the Witwatersrand,
Johannesburg, 2050 Wits, South Africa  +27 11 717-6181  fax: +27 11 717-6199



From ajb at ebi.ac.uk  Tue Jul 17 08:00:36 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Tue, 17 Jul 2007 09:00:36 +0100 (BST)
Subject: [EMBOSS] EST clustering program
In-Reply-To: <20070717065805.M59277@cs.wits.ac.za>
References: <20070717065805.M59277@cs.wits.ac.za>
Message-ID: <43677.81.98.241.17.1184659236.squirrel@webmail.ebi.ac.uk>

Dear Scott,

Sounds good.
The usual route would be to submit it to the
emboss-submit at emboss.open-bio.org list (which will reach all
members of the EMBOSS core team) and then communicate with
whoever gets in touch with you. These days we'd tend to make wrappers
available as EMBASSY packages.

Alan


>
>
> One of the applications listed in the suggested list for EMBOSS is a
> program that does
> clustering. We've been working on such a program with collaborators
> (mainly for ESTs)
> and we've recently developed an EMBOSS wrapper for it. Is there any way of
> making it
> available to the community?
>
> Scott
>
>
> ---- Scott Hazelhurst ------------------------  scott at cs.wits.ac.za
> --------
> Bioinformatics & Computer Science, University of the Witwatersrand,
> Johannesburg, 2050 Wits, South Africa  +27 11 717-6181  fax: +27 11
> 717-6199
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>




From rvijayasatya at ncifcrf.gov  Tue Jul 17 21:41:24 2007
From: rvijayasatya at ncifcrf.gov (Ravi Vijaya Satya)
Date: Tue, 17 Jul 2007 17:41:24 -0400
Subject: [EMBOSS] Database too lare for dbifasta
Message-ID: <000001c7c8bb$392f28e0$34572b81@0093Ravi>

Hello,

I am trying to index a large fasta file using dbifasta. He file is 18+GB in
size. Indexing with dbifasta was working fine with EMBOSS-4.0.0. However,
with 4.1.0 or 5.0.0, it complains that the file is 'too large for DBI
indexing. Any suggestions other than switching back to 4.0.0? 

Thanks,
Ravi




From georgios at biotek.uio.no  Wed Jul 18 07:23:28 2007
From: georgios at biotek.uio.no (George Magklaras)
Date: Wed, 18 Jul 2007 09:23:28 +0200
Subject: [EMBOSS] Database too lare for dbifasta
In-Reply-To: <000001c7c8bb$392f28e0$34572b81@0093Ravi>
References: <000001c7c8bb$392f28e0$34572b81@0093Ravi>
Message-ID: <469DBFF0.3020608@biotek.uio.no>

This comes from the nucleus library embdbi.c file.

if(ajFileLength(name) > (ajlong) INT_MAX)
           ajDie("File '%S' too large for DBI indexing", name);


INT_MAX is normally something like #  define INT_MAX       2147483647
, as defined by your /usr/include/limits.h file.

In plain English, this means that you will have to split your flat input 
data files so they are smaller than 2 Gigs. For EMBL database raw files 
, the EMBOSS distribution includes now the 'emblsplit.pl' file , under 
the scripts/ subdirectory. This script splits an #EMBL file (.dat)# your 
pass it into < 2 Gig chunks. This won't work for fasta files, it works 
only for EMBL format so you will have to split your 18 Gigs fasta input 
by other means.

In previous versions of EMBOSS (4.0.0), the DBI formatting appear to 
work, but the emboss index was not right, if your flat input file 
exceeded 2 Gigs. At least, I had problems with indexing EMBL format 
files larger than 2 Gigs and the dbiflat program.

Question to the developers:

Why INT_MAX (signed)? Why not unsigned UINT_MAX (to raise it a bit) or 
another raised limit? It is a bit of an overhead to have to go through 
the file split stage.

Best Regards,
GM

Ravi Vijaya Satya wrote:
> Hello,
> 
> I am trying to index a large fasta file using dbifasta. He file is 18+GB in
> size. Indexing with dbifasta was working fine with EMBOSS-4.0.0. However,
> with 4.1.0 or 5.0.0, it complains that the file is 'too large for DBI
> indexing. Any suggestions other than switching back to 4.0.0? 
> 
> Thanks,
> Ravi
> 
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
> 

-- 
--
George Magklaras

Senior Computer Systems Engineer/UNIX Systems Administrator
EMBnet Technical Management Board
The Biotechnology Centre of Oslo,
University of Oslo
http://www.biotek.uio.no/

EMBnet Norway:	http://www.no.embnet.org/


From ajb at ebi.ac.uk  Wed Jul 18 07:45:24 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 18 Jul 2007 08:45:24 +0100 (BST)
Subject: [EMBOSS] Database too lare for dbifasta
In-Reply-To: <000001c7c8bb$392f28e0$34572b81@0093Ravi>
References: <000001c7c8bb$392f28e0$34572b81@0093Ravi>
Message-ID: <54178.81.98.241.17.1184744724.squirrel@webmail.ebi.ac.uk>

Hello Ravi,

For files >2Gb you should use the dbx* applications for indexing e.g.
dbxfasta. It is likely that dbifasta in EMBOSS 4.0.0 just appeared
to work for large files but that entries past the 2Gb limit would
not be correctly retrieved.

HTH

Alan

> Hello,
>
> I am trying to index a large fasta file using dbifasta. He file is 18+GB
> in
> size. Indexing with dbifasta was working fine with EMBOSS-4.0.0. However,
> with 4.1.0 or 5.0.0, it complains that the file is 'too large for DBI
> indexing. Any suggestions other than switching back to 4.0.0?
>
> Thanks,
> Ravi
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>




From georgios at biotek.uio.no  Wed Jul 18 09:30:32 2007
From: georgios at biotek.uio.no (George Magklaras)
Date: Wed, 18 Jul 2007 11:30:32 +0200
Subject: [EMBOSS] Database too lare for dbifasta
In-Reply-To: <54178.81.98.241.17.1184744724.squirrel@webmail.ebi.ac.uk>
References: <000001c7c8bb$392f28e0$34572b81@0093Ravi>
	<54178.81.98.241.17.1184744724.squirrel@webmail.ebi.ac.uk>
Message-ID: <469DDDB8.5080005@biotek.uio.no>



ajb at ebi.ac.uk wrote:
 > Hello Ravi,
 >
 > For files >2Gb you should use the dbx* applications for indexing e.g.
 > dbxfasta.


Is it possible to highlight this in the EMBOSS manuals somehow? 
Application manual pages for the dbx utilities that mention the over 2 
Gbyte capability do of course exist, but the 2G limit is not mentioned 
in the respective manual pages of the dbi utils ('Known Bugs' for 
instance). So, if you have someone that reads the admin manual, he/she 
goes to dbi and not the dbx utils by default.

(If such a reference exists I apologize, but I can't see it. My comments 
refer to 'tfm' manual output for up to version 4.1.0 and the on-line 
manual on URL: http://emboss.sourceforge.net/docs/adminguide/admin.html ).

GM



From ajb at ebi.ac.uk  Wed Jul 18 10:03:44 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 18 Jul 2007 11:03:44 +0100 (BST)
Subject: [EMBOSS] Database too lare for dbifasta
In-Reply-To: <469DDDB8.5080005@biotek.uio.no>
References: <000001c7c8bb$392f28e0$34572b81@0093Ravi>
	<54178.81.98.241.17.1184744724.squirrel@webmail.ebi.ac.uk>
	<469DDDB8.5080005@biotek.uio.no>
Message-ID: <48767.81.98.241.17.1184753024.squirrel@webmail.ebi.ac.uk>


> Is it possible to highlight this in the EMBOSS manuals somehow?

I've copied this request on to the rest of the developers on
the emboss-bug list.

In answer to a previous question wrt UINT_MAX. That would, of course,
have been possible but the new indexing software had already been
written by then (or, at least, was well advanced) so it wasn't deemed
to be a high priority.

HTH

Alan




From rvijayasatya at ncifcrf.gov  Wed Jul 18 13:37:45 2007
From: rvijayasatya at ncifcrf.gov (Ravi Vijaya Satya)
Date: Wed, 18 Jul 2007 09:37:45 -0400
Subject: [EMBOSS] Database too lare for dbifasta
In-Reply-To: <48767.81.98.241.17.1184753024.squirrel@webmail.ebi.ac.uk>
References: <000001c7c8bb$392f28e0$34572b81@0093Ravi><54178.81.98.241.17.1184744724.squirrel@webmail.ebi.ac.uk><469DDDB8.5080005@biotek.uio.no>
	<48767.81.98.241.17.1184753024.squirrel@webmail.ebi.ac.uk>
Message-ID: <000001c7c940$d2e659b0$34572b81@0093Ravi>

 Thanks for all the information. 

Are there any limits on individual file size in dbxfasta? 

Thanks,
Ravi

-----Original Message-----
From: emboss-bounces at lists.open-bio.org
[mailto:emboss-bounces at lists.open-bio.org] On Behalf Of ajb at ebi.ac.uk
Sent: Wednesday, July 18, 2007 6:04 AM
To: emboss at emboss.open-bio.org
Subject: Re: [EMBOSS] Database too lare for dbifasta


> Is it possible to highlight this in the EMBOSS manuals somehow?

I've copied this request on to the rest of the developers on the emboss-bug
list.

In answer to a previous question wrt UINT_MAX. That would, of course, have
been possible but the new indexing software had already been written by then
(or, at least, was well advanced) so it wasn't deemed to be a high priority.

HTH

Alan


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



From ajb at ebi.ac.uk  Wed Jul 18 14:25:11 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 18 Jul 2007 15:25:11 +0100 (BST)
Subject: [EMBOSS] Database too lare for dbifasta
In-Reply-To: <000001c7c940$d2e659b0$34572b81@0093Ravi>
References: <000001c7c8bb$392f28e0$34572b81@0093Ravi><54178.81.98.241.17.1184744724.squirrel@webmail.ebi.ac.uk><469DDDB8.5080005@biotek.uio.no>
	<48767.81.98.241.17.1184753024.squirrel@webmail.ebi.ac.uk>
	<000001c7c940$d2e659b0$34572b81@0093Ravi>
Message-ID: <42904.81.98.241.17.1184768711.squirrel@webmail.ebi.ac.uk>


> Are there any limits on individual file size in dbxfasta?

64 bits for the dbx* applications rather than 32 bits for the dbi* ones
(give or take a single bit for sign as has already been mentioned).

Alan




From nycademon at spiralrealm.com  Wed Jul 18 17:32:20 2007
From: nycademon at spiralrealm.com (Guido N. Vacano)
Date: Wed, 18 Jul 2007 11:32:20 -0600
Subject: [EMBOSS] JASPAR
Message-ID: <469E4EA4.6000600@spiralrealm.com>

Hello--

    What would be involved in using the JASPAR database
(http://jaspar.genereg.net/) with EMBOSS? The TRANSFAC database is not
available for download (not without paying a hefty fee anyway), which
limits the utility of the tfscan program.

Thanks,
Guido Vacano


From ajb at ebi.ac.uk  Wed Jul 18 19:42:57 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 18 Jul 2007 20:42:57 +0100 (BST)
Subject: [EMBOSS] JASPAR
In-Reply-To: <469E4EA4.6000600@spiralrealm.com>
References: <469E4EA4.6000600@spiralrealm.com>
Message-ID: <35912.81.98.241.17.1184787777.squirrel@webmail.ebi.ac.uk>

Dear Guido,

Very little work from the look of it. The same technique is already
used on the protein side by the 'profit' program so it should be a
simple adaptation.

It looks like a good candidate for 5.1.0

HTH

Alan


> Hello--
>
>     What would be involved in using the JASPAR database
> (http://jaspar.genereg.net/) with EMBOSS? The TRANSFAC database is not
> available for download (not without paying a hefty fee anyway), which
> limits the utility of the tfscan program.
>
> Thanks,
> Guido Vacano
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>




From Richard.Rothery at ualberta.ca  Wed Jul 18 19:41:58 2007
From: Richard.Rothery at ualberta.ca (Richard Rothery)
Date: Wed, 18 Jul 2007 13:41:58 -0600
Subject: [EMBOSS] Extracting sequences from PDB files.....
In-Reply-To: <469E4EA4.6000600@spiralrealm.com>
Message-ID: <000301c7c973$b4858620$5e068081@Nordegg>

I would like to extract a primary sequence from a local "new" pdb file
that is a model based on a swissprot/uniprot sequence. I would like to
be able to assess the completeness of the model. Is there an EMBOSS
program that will do this?

Thanks,

Richard Rothery

###############################################
CIHR Molecular Biology of Membrane Proteins Group,
Department of Biochemistry, University of Alberta,
Edmonton T6G 2H7
Ph. (780) 492-2229 Fax. (780) 492-0886
###############################################


-----Original Message-----
From: emboss-bounces at lists.open-bio.org
[mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Guido N. Vacano
Sent: Wednesday, July 18, 2007 11:32 AM
To: EMBOSS Mailing List
Subject: [EMBOSS] JASPAR

Hello--

    What would be involved in using the JASPAR database
(http://jaspar.genereg.net/) with EMBOSS? The TRANSFAC database is not
available for download (not without paying a hefty fee anyway), which
limits the utility of the tfscan program.

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



From dksamuel at gmail.com  Thu Jul 19 04:11:25 2007
From: dksamuel at gmail.com (Duleep Samuel)
Date: Thu, 19 Jul 2007 09:41:25 +0530
Subject: [EMBOSS] JASPAR
In-Reply-To: <35912.81.98.241.17.1184787777.squirrel@webmail.ebi.ac.uk>
References: <469E4EA4.6000600@spiralrealm.com>
	<35912.81.98.241.17.1184787777.squirrel@webmail.ebi.ac.uk>
Message-ID: <a0bf33d50707182111u2d5a79a0qbb6000d62d2349b0@mail.gmail.com>

Sir, Please can mEMBOSS 5.10 be made to read and write pdb files, and play /
convert the the NCBI Cn3d to avi (It helps to understand structures easily)
thanks Samuel

On 7/19/07, ajb at ebi.ac.uk <ajb at ebi.ac.uk> wrote:
>
> Dear Guido,
>
> Very little work from the look of it. The same technique is already
> used on the protein side by the 'profit' program so it should be a
> simple adaptation.
>
> It looks like a good candidate for 5.1.0
>
> HTH
>
> Alan
>
>
> > Hello--
> >
> >     What would be involved in using the JASPAR database
> > (http://jaspar.genereg.net/) with EMBOSS? The TRANSFAC database is not
> > available for download (not without paying a hefty fee anyway), which
> > limits the utility of the tfscan program.
> >
> > Thanks,
> > Guido Vacano
> > _______________________________________________
> > 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 yogi.sundaravadanam at agrf.org.au  Thu Jul 19 05:20:02 2007
From: yogi.sundaravadanam at agrf.org.au (Yogi Sundaravadanam)
Date: Thu, 19 Jul 2007 15:20:02 +1000
Subject: [EMBOSS] Sixpack
In-Reply-To: <469B8E2A.50103@id.unizh.ch>
Message-ID: <H0000294002c3013.1184822401.mailmaster.agrf.org.au@MHS>


Hello all

Does anyone know if the sixpack in the new version of EMBOSS has an option for alternate translation (just like transeq -alternative)? 

Thanks heaps
Yogi
 
 




From REBA at hadassah.org.il  Thu Jul 19 06:55:42 2007
From: REBA at hadassah.org.il (??????? ???? - CONDIOTTI REBA)
Date: Thu, 19 Jul 2007 08:55:42 +0200
Subject: [EMBOSS] meme and mast
Message-ID: <9382027D01ABA04C92708FF63D4EFB2103D4419F@EXCHANGE.DOM.HADASSAH.ORG.IL>

I have two groups of DNA sequences. I want to look for consensus sequences in the first group with meme (which I have been able to do) and then look for that consensus sequence in the second group using mast. I have not been able to find the right command line to do this. 
Any help will be much appreciated.
Reba
 
Reba Condiotti
Goldyne Savad Institute of Gene Therapy
Hadassah University Hospital
POB 12000
Jerusalem 91120 Israel
Tel: 972-2-677-7927
FAX: 972-2-643-0982 






************************************************************************************
This footnote confirms that this email message has been scanned by
PineApp Mail-SeCure for the presence of malicious code, vandals & computer viruses.
************************************************************************************





From pmr at ebi.ac.uk  Thu Jul 19 06:47:28 2007
From: pmr at ebi.ac.uk (Peter Rice)
Date: Thu, 19 Jul 2007 07:47:28 +0100
Subject: [EMBOSS] Database too lare for dbifasta
In-Reply-To: <469DBFF0.3020608@biotek.uio.no>
References: <000001c7c8bb$392f28e0$34572b81@0093Ravi>
	<469DBFF0.3020608@biotek.uio.no>
Message-ID: <469F0900.4050807@ebi.ac.uk>

George Magklaras wrote:

> Question to the developers:
> 
> Why INT_MAX (signed)? Why not unsigned UINT_MAX (to raise it a bit) or 
> another raised limit? It is a bit of an overhead to have to go through 
> the file split stage.

The index file format was originally defined that way by the Staden 
package, and also used by EMBL/EBI CD-ROM indexing and by utilities at 
the Sanger Centre/Institute.

The dbi* index files have two problems - they cannot store file 
positions larger than 2Gb aqnd they do not allow duplicate primary 
identifiers.

We may remove them in a future release - but for smaller databases many 
users seem to find them useful still.

regards,

Peter


From niels at genomics.dk  Fri Jul 20 22:21:55 2007
From: niels at genomics.dk (Niels Larsen)
Date: Sat, 21 Jul 2007 00:21:55 +0200
Subject: [EMBOSS] EMBOSS 5.0
In-Reply-To: <35912.81.98.241.17.1184787777.squirrel@webmail.ebi.ac.uk>
References: <469E4EA4.6000600@spiralrealm.com>
	<35912.81.98.241.17.1184787777.squirrel@webmail.ebi.ac.uk>
Message-ID: <46A13583.4060708@genomics.dk>

Thank you for v5.0 (I have compile-ok on Mandriva Linux 2005 and
Ubuntu Linux 6.06 server version.)

Below are my observations from trying install EMBL locally; I did
it my own way in the end, so maybe not so useful for this list. I
do not need very fast entry access, just a local cache that avoids
request-flooding EBI/NCBI for entries and reduces network traffic.

First I tried dbxflat. It works fine, but indexing takes time; I
estimated a weeks run-time to index the release, and close to a
day for the daily updates on the average (the planned incremental
indexing will help). This means there has to be a machine dedicated
to keep EMBL up to date, because it is cpu-bound. Not unreasonable,
but I wanted to have it work on a cheapo external harddrive, say,
and for it to be ready sooner.

Then I tried BioPerl. It looked like 3 weeks for that run to finish,
so not workable. I have not looked how many entries change between
releases, but having the new release built soon after its available
must be good.

Then I tried to put each record in directories derived from their
accession number: AACI02000001 would be put in AACI/0200, AX101010
in AX1/010, and so on. Each directory has a two column table
(LOOKUP_LIST) with lines like these,

AACI02000001.1  1
AACI02000002.1  1
AACI02000003.1  1
AACI02000004.1  2
AACI02000005.1  2
AACI02000006.1  2
AACI02000007.1  2

where column 1 is the versioned accession number and the second is
the file name that contains its corresponding entry. The entry
files are gzip-compressed and named 1.gz, 2.gz, etc. The release
files stay compressed and are deleted after splitting, so the total
extra space required does not exceed 20% or so of the distribution
size. Creation time is about 26 hours and a typical daily-file is
2-4 minutes; download and import can run in parallel (not done by
threads of course, but by launching the script twice). I tried to
make a balance between disk and ram by caching file handles etc,
but ram does not exceed 330 mb at any time (and stays much lower
most of the time). To access a record, I do "zcat $file | seqret
..... " which is then parsed by bioperl. The access time varies
between 0.03 seconds to 0.3 seconds depending on size, time since
last access, speed of the disk, compression ratio and logic,
humidity outside etc.

Well, I may again have redone something, but at least it filled my
little need. I dont know if others have had the same, or if it is
a feature that EMBOSS should have.

Niels L

PS - one of my mistakes was to get a big slow USB-2 drive under
Linux. The drive is ok, but the ext3 file system broke completely.
I was advised to use firewire or ATA/SATA instead, which allows
health-monitoring with smartctl et al as well (USB does not).


From charles-listes-emboss at plessy.org  Sun Jul 22 10:55:17 2007
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Sun, 22 Jul 2007 19:55:17 +0900
Subject: [EMBOSS] EMBOSS 5.0.0 available as a Debian package.
In-Reply-To: <54666.81.98.241.17.1184486717.squirrel@webmail.ebi.ac.uk>
References: <54666.81.98.241.17.1184486717.squirrel@webmail.ebi.ac.uk>
Message-ID: <20070722105517.GC21806@kunpuu.plessy.org>

Le Sun, Jul 15, 2007 at 09:05:17AM +0100, ajb at ebi.ac.uk a ?crit :
> 1) UNIX
> 
> EMBOSS 5.0.0 for UNIXen is now available from the usual ftp server i.e.
> 
>        ftp://emboss.open-bio.org/pub/EMBOSS/

Dear all,

I am very happy to announce that since this release 5.0.0, the
Debian-Med project provides binary packages for EMBOSS.

Installation on Debian is now as easy as "aptitude install emboss".  By
default, Debian's tool "aptitude" will also install dialign and primer3,
so that the wrappers can work out of the box[1]. For clustalw, due to
licence issues, you will need to add the "non-free" category to your
package list, and "aptitude install clustalw"

Debian's package for EMBOSS has been tested as an experimental package
for version 4.1.0 and is expected to be stable. However, it still has
the following limitations:
 - Since the pcre_internal.h header is not shipped in the "emboss-libs"
   package, compiling external apps will be difficult (but we are
   working on this).
 - EMBASSY is not yet available.
 - Java support is disabled by default.
 - The "cons" and "pscan" had to be renamed "em_cons" and "em_pscan"
   because other programs with this name are already in Debian. However,
   we provide an additional path, /usr/lib/emboss, in which we guarantee
   that names will always be unchanged.

Debian packages for EMBOSS provide a manpage for each program. They are
autobuilt from the acd files, and their informational content is a bit
higher than the --help option, and lower than the tfm manual.

In addition to EMBOSS, we also packaged the emboss-explorer frontend.
Just "apt-get install emboss-explorer" and enjoy it at:
http://localhost/emboss-explorer

We are now working on packaging the EMBASSY programs.

Have a nice day,

Charles Plessy, for the Debian-Med packaging team.

[1] After writing this email, I realised that edialign dissapeared in
    EMBOSS 5.0.0. An updated package will be uploaded, which does not
    depend on dialign.

-- 
Charles Plessy
Debian-Med packaging team
Wako, Saitama, Japan


From sbassi at gmail.com  Sun Jul 22 18:53:22 2007
From: sbassi at gmail.com (Sebastian Bassi)
Date: Sun, 22 Jul 2007 15:53:22 -0300
Subject: [EMBOSS] EMBOSS 5.0.0 available as a Debian package.
In-Reply-To: <20070722105517.GC21806@kunpuu.plessy.org>
References: <54666.81.98.241.17.1184486717.squirrel@webmail.ebi.ac.uk>
	<20070722105517.GC21806@kunpuu.plessy.org>
Message-ID: <b43bf2080707221153i55357922qd02df3a7f0b6c464@mail.gmail.com>

On 7/22/07, Charles Plessy <charles-listes-emboss at plessy.org> wrote:
> I am very happy to announce that since this release 5.0.0, the
> Debian-Med project provides binary packages for EMBOSS.

This is a very nice news!!.
This package works also on Ubuntu?
Best,
SB.

-- 
Bioinformatics news: http://www.bioinformatica.info
Lriser: http://www.linspire.com/lraiser_success.php?serial=318


From charles-listes-emboss at plessy.org  Mon Jul 23 00:33:21 2007
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Mon, 23 Jul 2007 09:33:21 +0900
Subject: [EMBOSS] EMBOSS 5.0.0 available as a Debian package.
In-Reply-To: <b43bf2080707221153i55357922qd02df3a7f0b6c464@mail.gmail.com>
References: <54666.81.98.241.17.1184486717.squirrel@webmail.ebi.ac.uk>
	<20070722105517.GC21806@kunpuu.plessy.org>
	<b43bf2080707221153i55357922qd02df3a7f0b6c464@mail.gmail.com>
Message-ID: <20070723003321.GA10302@kunpuu.plessy.org>

Le Sun, Jul 22, 2007 at 03:53:22PM -0300, Sebastian Bassi a ?crit :
> On 7/22/07, Charles Plessy <charles-listes-emboss at plessy.org> wrote:
> > I am very happy to announce that since this release 5.0.0, the
> > Debian-Med project provides binary packages for EMBOSS.
> 
> This is a very nice news!!.
> This package works also on Ubuntu?

I do not know : I have no Ubuntu to test the binary packages. However,
the source package should be able to produce Ubuntu binary packages
without problems. (Same for Linspire, as you seem to be interested in).

If you are not in a hurry, maybe the easiest way to get emboss in Ubuntu
would be to request it to the MOTU science. Here is a mailing list they
read:

http://lists.tauware.de/listinfo/ubuntu-science

Also, there must be for sure a way to use Launchpad, but I do not know
it...

Have a nice day,

-- 
Charles


From golharam at umdnj.edu  Mon Jul 23 14:56:54 2007
From: golharam at umdnj.edu (Ryan Golhar)
Date: Mon, 23 Jul 2007 10:56:54 -0400
Subject: [EMBOSS] New mEMBOSS on ftp server
In-Reply-To: <41376.81.98.241.17.1184583384.squirrel@webmail.ebi.ac.uk>
Message-ID: <005501c7cd39$b5728640$2d01a8c0@PICO>

What is mEMBOSS?  I'm not familiar with this one and do not see if on the
website

-----Original Message-----
From: emboss-bounces at lists.open-bio.org
[mailto:emboss-bounces at lists.open-bio.org] On Behalf Of ajb at ebi.ac.uk
Sent: Monday, July 16, 2007 6:56 AM
To: emboss-announce at emboss.open-bio.org
Cc: emboss at emboss.open-bio.org
Subject: [EMBOSS] New mEMBOSS on ftp server


A new version of mEMBOSS-5.0.0-setup.exe has been put on the ftp server
(filename unchanged as it is just an enhancement).

It had been noticed that the original version only worked if your Java was
up-to-date (1.6 u2). This new version should also work with Java 1.4 and
Java 1.5. Furthermore, it will auto-detect the Java location and halt
installation if Java is not found.

Alan


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




From golharam at umdnj.edu  Mon Jul 23 15:56:43 2007
From: golharam at umdnj.edu (Ryan Golhar)
Date: Mon, 23 Jul 2007 11:56:43 -0400
Subject: [EMBOSS] EMBOSS 5.0.0 RPMs available
In-Reply-To: <55352.81.98.241.17.1184486754.squirrel@webmail.ebi.ac.uk>
Message-ID: <005a01c7cd42$132efa90$2d01a8c0@PICO>

RPMs for EMBOSS 5.0.0 and the EMBASSY suite are now available at
http://informatics.umdnj.edu/BioRPMs/



-----Original Message-----
From: emboss-bounces at lists.open-bio.org
[mailto:emboss-bounces at lists.open-bio.org] On Behalf Of ajb at ebi.ac.uk
Sent: Sunday, July 15, 2007 4:06 AM
To: emboss at emboss.open-bio.org
Subject: [EMBOSS] EMBOSS 5.0.0 released


1) UNIX

EMBOSS 5.0.0 for UNIXen is now available from the usual ftp server i.e.

       ftp://emboss.open-bio.org/pub/EMBOSS/

as the file EMBOSS-5.0.0.tar.gz . The EMBASSY packages are available in the
same directory. Remember that EMBASSY packages are tailored for each major
release of EMBASSY: do not try to reuse versions from previous EMBOSS
releases.

The sourceforge web pages will be updated tomorrow to show version 5
applications by default. For now they can be accessed explicitly at:
http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/

2) Windows

The Microsoft Windows version is now called mEMBOSS and installs with a
standalone version of Jemboss as a GUI; command line gurus can still use a
command window of course. You must first install Java from java.sun.com (or
java.com) and the vcredist_x86.exe file from the EMBOSS ftp server or the
Microsoft web site (N.B. the latter file is a new version with the current
release, previous releases from the ftp server will not work). mEMBOSS and
vcredist_x86.exe are available in:

       ftp://emboss.open-bio.org/pub/EMBOSS/windows/

Please use the name mEMBOSS (not EMBOSS or EMBOSSWIN) when asking any
questions about the Windows version on the EMBOSS mailing lists. mEMBOSS has
been developed under XP and tested under XP and VISTA, though it will likely
work under several other Windows versions.

3) Changes
See the ChangeLog file

4) Support libraries

UNIX users who use the optional PNG graphics should check that they have a
GD version 2 library (homepage www.libgd.org) installed. GD v1 libraries
will not work correctly with EMBOSS 5.0.0. EMBOSS now uses both PNG and GIF
routines from the GD library. EMBOSS has been tested using GD versions
2.0.33, 2.0.34 and 2.0.35, though some older version 2 libraries should also
work.


Alan


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




From jmullersman at yahoo.com  Mon Jul 23 18:05:00 2007
From: jmullersman at yahoo.com (Jerry Mullersman)
Date: Mon, 23 Jul 2007 11:05:00 -0700 (PDT)
Subject: [EMBOSS] New mEMBOSS on ftp server
In-Reply-To: <005501c7cd39$b5728640$2d01a8c0@PICO>
Message-ID: <527413.86323.qm@web43138.mail.sp1.yahoo.com>

Ryan,

Per the original announcement of EMBOSS 5.0.0, mEMBOSS is the new designation of the Windows version of EMBOSS; see the announcement excerpt below:


2) Windows

The Microsoft Windows version is now called mEMBOSS and installs with a
standalone version of Jemboss as a GUI; command line gurus can still use a
command window of course. You must first install Java from java.sun.com (or
java.com) and the vcredist_x86.exe file from the EMBOSS ftp server or the
Microsoft web site (N.B. the latter file is a new version with the current
release, previous releases from the ftp server will not work). mEMBOSS and
vcredist_x86.exe are available in:

       ftp://emboss.open-bio.org/pub/EMBOSS/windows/

Please use the name mEMBOSS (not EMBOSS or EMBOSSWIN) when asking any
questions about the Windows version on the EMBOSS mailing lists. mEMBOSS has
been developed under XP and tested under XP and VISTA, though it will likely
work under several other Windows versions.

Cheers,

Jerry Mullersman



Ryan Golhar <golharam at umdnj.edu> wrote: What is mEMBOSS?  I'm not familiar with this one and do not see if on the
website

-----Original Message-----
From: emboss-bounces at lists.open-bio.org
[mailto:emboss-bounces at lists.open-bio.org] On Behalf Of ajb at ebi.ac.uk
Sent: Monday, July 16, 2007 6:56 AM
To: emboss-announce at emboss.open-bio.org
Cc: emboss at emboss.open-bio.org
Subject: [EMBOSS] New mEMBOSS on ftp server


A new version of mEMBOSS-5.0.0-setup.exe has been put on the ftp server
(filename unchanged as it is just an enhancement).

It had been noticed that the original version only worked if your Java was
up-to-date (1.6 u2). This new version should also work with Java 1.4 and
Java 1.5. Furthermore, it will auto-detect the Java location and halt
installation if Java is not found.

Alan


_______________________________________________
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



Jerald E. Mullersman, MD, PhD
Associate Professor
Department of Pathology
East Tennessee State University
PO Box 70568
Johnson City, TN 37614
phone: (423) 439-6210   fax:  (423) 439-8060


From Ethan.Hack at ncl.ac.uk  Tue Jul 24 08:28:01 2007
From: Ethan.Hack at ncl.ac.uk (E. Hack)
Date: Tue, 24 Jul 2007 09:28:01 +0100 (GMT Standard Time)
Subject: [EMBOSS] mEMBOSS: Jemboss and proxy servers
Message-ID: <Pine.WNT.4.64.0707240909410.2028@mach12.campus.ncl.ac.uk>

I have installed the new Windows mEMBOSS.  To use external databases, I 
have to connect to the web via a proxy server.  When running EMBOSS 
programs from a Windows command prompt, I can do this successfully using 
the EMBOSS_PROXY environment variable.  With Jemboss, however, external 
connections to databases give me a "socket connect failed" error 
message, and I can't reach external help files either.

The default setting in my Java Control Panel is "Use browser settings". 
I have tried changing this to "Use proxy server" and I have also tried 
specifying the proxy server from inside Jemboss under Preferences - 
Jemboss - Browser Proxies.  Neither of these methods seems to make any 
difference.

I'd be grateful for any suggestions as to what the problem might be. I 
hope the question is an appropriate use of this mailing list and 
apologise if it isn't.  I suspect the solution may be helpful to others 
too (even it should be obvious...) - I don't think there's anything 
particularly unusual about the way my computer is set up.

Ethan Hack

-- 
Dr Ethan Hack                           | E-mail: Ethan.Hack at ncl.ac.uk
School of Biology and Psychology        | Phone:  +44 191 222 8576
Newcastle University                    | Fax:    +44 191 222 5228
Newcastle upon Tyne  NE1 7RU, UK


From Ethan.Hack at ncl.ac.uk  Tue Jul 24 11:01:51 2007
From: Ethan.Hack at ncl.ac.uk (E. Hack)
Date: Tue, 24 Jul 2007 12:01:51 +0100 (GMT Standard Time)
Subject: [EMBOSS] [Fwd:  mEMBOSS: Jemboss and proxy servers]
In-Reply-To: <C2CB91D9.50B2E%tjc@sanger.ac.uk>
References: <C2CB91D9.50B2E%tjc@sanger.ac.uk>
Message-ID: <Pine.WNT.4.64.0707241152290.1340@mach12.campus.ncl.ac.uk>

Perfect!  Problem solved.  I think it would be worth adding this 
information somewhere conspicuous (for Windows, the README.win file 
would be good, as it has high visibility) - everything else in the 
installation is pretty much automatic.

Thanks very much.

Ethan Hack

On Tue, 24 Jul 2007, you wrote:

> Hi Ethan
>
> Try editing the jemboss.properties file in :
> mEMBOSS\jemboss\jar\resources\jemboss.properties
>
> And add EMBOSS_PROXY to the embossEnvironment entry, see the documentation
> for the jemboss.properties file at:
>
> http://emboss.sourceforge.net/Jemboss/install/properties.html
>
> So try adding a line like this:
>
> embossEnvironment=EMBOSS_PROXY=wwwcache.ncl.ac.uk:8080
>
> Then re-run Jemboss. If this works you should be able to access external
> databases.
>
> To get the jemboss browser working for the help files I think you can just
> edit the properties of the jemboss shortcut on your desktop and add "java
> -DproxyHost= wwwcache.ncl.ac.uk -DproxyPort=8080 -jar ..." to the start of
> the Target: field.
>
> Regards
> Tim
>
>
> On 24/7/07 10:25, "ajb at ebi.ac.uk" <ajb at ebi.ac.uk> wrote:
>
>
>> ---------------------------- Original Message ----------------------------
>> Subject: [EMBOSS] mEMBOSS: Jemboss and proxy servers
>> From:    "E. Hack" <Ethan.Hack at ncl.ac.uk>
>> Date:    Tue, July 24, 2007 9:28 am
>> To:      emboss at lists.open-bio.org
>> --------------------------------------------------------------------------
>>
>> I have installed the new Windows mEMBOSS.  To use external databases, I
>> have to connect to the web via a proxy server.  When running EMBOSS
>> programs from a Windows command prompt, I can do this successfully using
>> the EMBOSS_PROXY environment variable.  With Jemboss, however, external
>> connections to databases give me a "socket connect failed" error
>> message, and I can't reach external help files either.
>>
>> The default setting in my Java Control Panel is "Use browser settings".
>> I have tried changing this to "Use proxy server" and I have also tried
>> specifying the proxy server from inside Jemboss under Preferences -
>> Jemboss - Browser Proxies.  Neither of these methods seems to make any
>> difference.
>>
>> I'd be grateful for any suggestions as to what the problem might be. I
>> hope the question is an appropriate use of this mailing list and
>> apologise if it isn't.  I suspect the solution may be helpful to others
>> too (even it should be obvious...) - I don't think there's anything
>> particularly unusual about the way my computer is set up.
>>
>> Ethan Hack

-- 
Dr Ethan Hack                           | E-mail: Ethan.Hack at ncl.ac.uk
School of Biology and Psychology        | Phone:  +44 191 222 8576
Newcastle University                    | Fax:    +44 191 222 5228
Newcastle upon Tyne  NE1 7RU, UK


From sbassi at gmail.com  Tue Jul 24 17:57:15 2007
From: sbassi at gmail.com (Sebastian Bassi)
Date: Tue, 24 Jul 2007 14:57:15 -0300
Subject: [EMBOSS] Problem making EMBOSS 5 in xubuntu
Message-ID: <b43bf2080707241057v3d6d7bbdy4cda28f15e601dfc@mail.gmail.com>

I tried to compile emboss 5 in Xubuntu and I got several errors. Since
the output is about 30Kb, I uploaded the output here to avoid filling
this list:

http://sbassi.googlepages.com/embosserror

I have compilers installed (by build-essential). Xubuntu uses XFCE as
xwindows windows manager.
Best,
SB.

-- 
Bioinformatics news: http://www.bioinformatica.info
Lriser: http://www.linspire.com/lraiser_success.php?serial=318


From sbassi at gmail.com  Tue Jul 24 18:25:08 2007
From: sbassi at gmail.com (Sebastian Bassi)
Date: Tue, 24 Jul 2007 15:25:08 -0300
Subject: [EMBOSS] Problem making EMBOSS 5 in xubuntu
In-Reply-To: <E1IDOnl-0005Pu-IQ@mendel.bio.caltech.edu>
References: <E1IDOnl-0005Pu-IQ@mendel.bio.caltech.edu>
Message-ID: <b43bf2080707241125y5bc08d62jbd7c939b456bfea5@mail.gmail.com>

On 7/24/07, David Mathog <mathog at caltech.edu> wrote:
> Does your system have Xlib.h?  On many linux distros the include
...
> libx11_6-devel-1.1.1-2.1mdv2007.1
....

Yes, the missing package was libx-dev. I installed and now it is
compiling (didn't finish yet).
Thank you very much,
Best,
SB.

-- 
Bioinformatics news: http://www.bioinformatica.info
Lriser: http://www.linspire.com/lraiser_success.php?serial=318


From mathog at caltech.edu  Tue Jul 24 18:08:05 2007
From: mathog at caltech.edu (David Mathog)
Date: Tue, 24 Jul 2007 11:08:05 -0700
Subject: [EMBOSS] Problem making EMBOSS 5 in xubuntu
Message-ID: <E1IDOnl-0005Pu-IQ@mendel.bio.caltech.edu>



> I tried to compile emboss 5 in Xubuntu and I got several errors. Since
> the output is about 30Kb, I uploaded the output here to avoid filling
> this list:
> 
> http://sbassi.googlepages.com/embosserror
> 
> I have compilers installed (by build-essential). Xubuntu uses XFCE as
> xwindows windows manager.

D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -MT
xwin.lo -MD -MP -MF .deps/xwin.Tpo -c xwin.c  -fPIC -DPIC -o .libs/xwin.o
In file included from xwin.c:34:
plxwd.h:22:22: error: X11/Xlib.h: No such file or directory
plxwd.h:23:23: error: X11/Xutil.h: No such file or directory
plxwd.h:24:28: error: X11/cursorfont.h: No such file or directory
plxwd.h:25:24: error: X11/keysym.h: No such file or directory

Does your system have Xlib.h?  On many linux distros the include
files are in separate packages which are not installed by default.
For instance on Mandriva:

% locate Xlib.h
/usr/include/X11/Xlib.h
% rpm -q --whatprovides /usr/include/X11/Xlib.h
libx11_6-devel-1.1.1-2.1mdv2007.1

If the files are installed you may need to give configure a hint
as to where to find them.  (That would be surprising in this case
though, those are pretty common include files.) 

Regards,

David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech


From bush at HMC.Edu  Thu Jul 26 16:44:00 2007
From: bush at HMC.Edu (Eliot Bush)
Date: Thu, 26 Jul 2007 09:44:00 -0700
Subject: [EMBOSS] relative abundance/word bias application
Message-ID: <46A8CF50.3040006@hmc.edu>

hello,

I'm wondering if people have any interest in including in EMBOSS an 
application to calculate the relative abundance/bias of words.

The measure I have in mind is that used by Karlin and others (for 
example in Burge, C. et al. PNAS 1992). It is the frequency of a 
particular word, divided by its expected frequency based on the 
frequencies of all its subwords, including gapped subwords. This gives 
you bias at a particular word size, removing the effects at smaller word 
sizes.

For small word sizes there are formulas which one can use, but as you 
get to larger sizes these get unwieldy. I've been working on some code 
which is able calculate this measure up to 10 or 11 bp words in 
reasonable amounts of time. If there is interest, I would be happy to 
contribute it.

Eliot



From simon.andrews at bbsrc.ac.uk  Fri Jul 27 08:24:19 2007
From: simon.andrews at bbsrc.ac.uk (Simon Andrews)
Date: Fri, 27 Jul 2007 09:24:19 +0100
Subject: [EMBOSS] relative abundance/word bias application
In-Reply-To: <46A8CF50.3040006@hmc.edu>
References: <46A8CF50.3040006@hmc.edu>
Message-ID: <E8429619-AD73-4473-8861-102E340DB67A@bbsrc.ac.uk>


On 26 Jul 2007, at 17:44, Eliot Bush wrote:

> hello,
>
> I'm wondering if people have any interest in including in EMBOSS an
> application to calculate the relative abundance/bias of words.
>
> I've been working on some code
> which is able calculate this measure up to 10 or 11 bp words in
> reasonable amounts of time. If there is interest, I would be happy to
> contribute it.

Yes, I was just discussing doing this kind of analysis yesterday.   
We'd certainly appreciate code in EMBOSS which could do this kind of  
calculation.

Cheers

Simon.



From ajb at ebi.ac.uk  Fri Jul 27 09:02:29 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Fri, 27 Jul 2007 10:02:29 +0100 (BST)
Subject: [EMBOSS] relative abundance/word bias application
In-Reply-To: <E8429619-AD73-4473-8861-102E340DB67A@bbsrc.ac.uk>
References: <46A8CF50.3040006@hmc.edu>
	<E8429619-AD73-4473-8861-102E340DB67A@bbsrc.ac.uk>
Message-ID: <58699.81.98.241.17.1185526949.squirrel@webmail.ebi.ac.uk>


> Yes, I was just discussing doing this kind of analysis yesterday.
> We'd certainly appreciate code in EMBOSS which could do this kind of
> calculation.

And, of course, we're more than happy to receive contributions to
EMBOSS.

Alan




From Perdeep.Mehta at STJUDE.ORG  Fri Jul 27 22:13:27 2007
From: Perdeep.Mehta at STJUDE.ORG (Mehta, Perdeep)
Date: Fri, 27 Jul 2007 17:13:27 -0500
Subject: [EMBOSS] help with Profit
Message-ID: <F2235647AC878D438F09255C39842FBC1BB70439@SJMEMXMB03.stjude.sjcrh.local>

Hi,

I am trying to search swissprot protein database with the "Profit"
program. Somehow after running for a while Profit produces following out
put that has no data in it. Here is the text in the generated output
file.

# PROF scan using Henikoff profile pdz_henikoff.prf
# Scores >= threshold 75 (max score 88.53)
#

Does any one have a clue what's wrong with it?  I checked the
installation of swissprot database it works fine I could fetch a
sequence out with seqret.

Thanks in advance for any help.
perdeep

Hartwell Center for Bioinformatics & Biotechnology
St. Jude Children's Research Hospital
Memphis, TN 38105-2794
Tel: 901-495 3774
http://www.hatwellcenter.org/



From zhangcg at bmi.ac.cn  Mon Jul 30 07:37:45 2007
From: zhangcg at bmi.ac.cn (Chenggang Zhang)
Date: Mon, 30 Jul 2007 15:37:45 +0800
Subject: [EMBOSS] EMBOSS 5.0.0 compilation fails on RedHat ver 9.0 (GD
	error)?
Message-ID: <200707301537437988523@bmi.ac.cn>

Dear EMBOSS maintainer,

I have the similary question as Christian reported below. However, even if I have updated the GD to version 2.0.28 or 2.0.35, I still failed to install the EMBOSS5 in my computer (uname information: Linux 2.4.20-8smp #1 SMP Thu Mar 13 17:45:54 EST 2003 i686 i686 i386 GNU/Linux, RedHat ver 9.0). The error information was attached below. Could you please tell me how to solve this question?

make[2]: Entering directory `/dev/shm/EMBOSS-5.0.0/emboss' 
/bin/sh ../libtool --tag=CC   --mode=link gcc  -O2   -o aaindexextract 
aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la 
../ajax/libajax.la ../plplot/libeplplot.la -L/usr/X11R6/lib -lX11  -lm  -lgd 
-lpng -lz -lm 
gcc -O2 -o .libs/aaindexextract aaindexextract.o ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so ../ajax/.libs/libajax.so ../plplot/.libs/libeplplot.so -L/usr/X11R6/lib -lX11 -lgd -lpng -lz -lm  -Wl,--rpath -Wl,/usr/local/emboss5/lib 
../plplot/.libs/libeplplot.so: undefined reference to `gdImageGifPtr' 
../plplot/.libs/libeplplot.so: undefined reference to `gdImageSetThickness' 
../plplot/.libs/libeplplot.so: undefined reference to `gdImagePngPtrEx' 
../plplot/.libs/libeplplot.so: undefined reference to `gdImageCreateTrueColor' 
../plplot/.libs/libeplplot.so: undefined reference to `gdImageSetAntiAliased' 
collect2: ld returned 1 exit status 
make[2]: *** [aaindexextract] Error 1 
make[2]: Leaving directory `/dev/shm/EMBOSS-5.0.0/emboss' 
make[1]: *** [all-recursive] Error 1 
make[1]: Leaving directory `/dev/shm/EMBOSS-5.0.0/emboss' 
make: *** [all-recursive] Error 1 

Best regards,

Sincerely yours,
Chenggang Zhang
2007.07.30 15:36:41

==============================================
Chenggang Zhang, PhD, Professor and Director
Department of Neurobiology
Beijing Institute of Radiation Medicine
Taiping Road 27, Beijing, 100850, China.
Tel: +8610-66931590. Fax: +8610-68169574
Cell phone: +8610-13910133213
Email: zhangcg at bmi.ac.cn,  zcgweb at 126.com
       zcgweb at gmail.com, zcgweb at yahoo.com
==============================================


>================================================================================================================
[EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif support
ajb at ebi.ac.uk ajb at ebi.ac.uk 
Mon Jul 16 12:23:47 EDT 2007 

Previous message: [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif support 
Next message: [EMBOSS] Sixpack 
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] 

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

Dear Christian,

Support for GIF was restored in gd 2.0.28 on July 21st, 2004. So, as
mentioned in the announcement, just install an up-to-date gd2 on SLES 9
and the compilation will work.

I've updated the development version of README to reflect this.

Alan



> Dear EMBOSS maintainer
>
> Compilation of EMBOSS 5.0.0 on SLES9 (with all graphical devel libs)
> fails, while linking:
>
> gcc -O2 -D__amd64__ -o .libs/aaindexextract aaindexextract.o
> ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so
> ../ajax/.libs/libajax.so ../plplot/.libs/libeplplot.so -L/usr/X11R6/lib64
> /usr/lib64/libgd.so -L/usr/lib64 -lXpm -lX11
> /usr/lib64/libjpeg.so /usr/lib64/libfreetype.so -lpng12 -lpng -lz -lm
> -Wl,--rpath -Wl,/usr/local/emboss5/lib
>
> ../plplot/.libs/libeplplot.so: undefined reference to `gdImageGifPtr'
>
> Configuration:
> ./configure --prefix=/usr/local/emboss5
>
> It seems for me that EMBOSS 5.0.0 is looking for GIF support despite of
> the fact that newer Versions of
> gd don't support gif anymore (cf. README line 65).
>
> Is there any workarround for the problem (I don't bother changing code)?
>
> Best regards
> Christian
> --
> =============================================================================
> Christian Bolliger
> IT Services                      | http://www.id.uzh.ch/
> Central Systems / HPC   	 | http://www.matterhorn.uzh.ch/
> University of  Zuerich           | E-Mail: christian.bolliger at id.uzh.ch
> Winterthurerstr. 190             | Tel: +41 (0)1 63 56775
> CH-8057 Zuerich; Switzerland     | Fax: +41 (0)1 63 54505
> Mime/S CA:                https://www.ca.unizh.ch/client/
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>




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


Previous message: [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif support 
Next message: [EMBOSS] Sixpack 
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] 

--------------------------------------------------------------------------------
More information about the EMBOSS mailing list




From ajb at ebi.ac.uk  Mon Jul 30 08:22:53 2007
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Mon, 30 Jul 2007 09:22:53 +0100 (BST)
Subject: [EMBOSS] EMBOSS 5.0.0 compilation fails on RedHat ver 9.0 (GD
 error)?
In-Reply-To: <200707301537437988523@bmi.ac.cn>
References: <200707301537437988523@bmi.ac.cn>
Message-ID: <37079.81.98.241.17.1185783773.squirrel@webmail.ebi.ac.uk>

Dear Chenggang Zhang,

There is insufficient detail in your message to be able to answer
it definitively, except to say that it is a GD error. In general:

1) If the GD update is from RPMs that put the gd and gd-devel
   files in the standard RH9 system area (unlikely I suppose as
   RH9 is so old) then you should just do a 'make clean' and
   './configure' EMBOSS again.

2) If you've compiled gd yourself and the libraries are
   in (e.g.) /usr/local/lib and the headers under /usr/local/include
   then, again, 'make clean' but this time add the
      --with-pngdriver=/usr/local
   switch to the './configure' line. (Amend /usr/local appropriately
   if you put the gd files elsewhere).

HTH

Alan

> Dear EMBOSS maintainer,
>
> I have the similary question as Christian reported below. However, even if
> I have updated the GD to version 2.0.28 or 2.0.35, I still failed to
> install the EMBOSS5 in my computer (uname information: Linux 2.4.20-8smp
> #1 SMP Thu Mar 13 17:45:54 EST 2003 i686 i686 i386 GNU/Linux, RedHat ver
> 9.0). The error information was attached below. Could you please tell me
> how to solve this question?
>
> make[2]: Entering directory `/dev/shm/EMBOSS-5.0.0/emboss'
> /bin/sh ../libtool --tag=CC   --mode=link gcc  -O2   -o aaindexextract
> aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la
> ../ajax/libajax.la ../plplot/libeplplot.la -L/usr/X11R6/lib -lX11  -lm
> -lgd
> -lpng -lz -lm
> gcc -O2 -o .libs/aaindexextract aaindexextract.o
> ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so
> ../ajax/.libs/libajax.so ../plplot/.libs/libeplplot.so -L/usr/X11R6/lib
> -lX11 -lgd -lpng -lz -lm  -Wl,--rpath -Wl,/usr/local/emboss5/lib
> ../plplot/.libs/libeplplot.so: undefined reference to `gdImageGifPtr'
> ../plplot/.libs/libeplplot.so: undefined reference to
> `gdImageSetThickness'
> ../plplot/.libs/libeplplot.so: undefined reference to `gdImagePngPtrEx'
> ../plplot/.libs/libeplplot.so: undefined reference to
> `gdImageCreateTrueColor'
> ../plplot/.libs/libeplplot.so: undefined reference to
> `gdImageSetAntiAliased'
> collect2: ld returned 1 exit status
> make[2]: *** [aaindexextract] Error 1
> make[2]: Leaving directory `/dev/shm/EMBOSS-5.0.0/emboss'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/dev/shm/EMBOSS-5.0.0/emboss'
> make: *** [all-recursive] Error 1
>
> Best regards,
>
> Sincerely yours,
> Chenggang Zhang
> 2007.07.30 15:36:41
>
> ==============================================
> Chenggang Zhang, PhD, Professor and Director
> Department of Neurobiology
> Beijing Institute of Radiation Medicine
> Taiping Road 27, Beijing, 100850, China.
> Tel: +8610-66931590. Fax: +8610-68169574
> Cell phone: +8610-13910133213
> Email: zhangcg at bmi.ac.cn,  zcgweb at 126.com
>        zcgweb at gmail.com, zcgweb at yahoo.com
> ==============================================
>
>
>>================================================================================================================
> [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif support
> ajb at ebi.ac.uk ajb at ebi.ac.uk
> Mon Jul 16 12:23:47 EDT 2007
>
> Previous message: [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif
> support
> Next message: [EMBOSS] Sixpack
> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>
> --------------------------------------------------------------------------------
>
> Dear Christian,
>
> Support for GIF was restored in gd 2.0.28 on July 21st, 2004. So, as
> mentioned in the announcement, just install an up-to-date gd2 on SLES 9
> and the compilation will work.
>
> I've updated the development version of README to reflect this.
>
> Alan
>
>
>
>> Dear EMBOSS maintainer
>>
>> Compilation of EMBOSS 5.0.0 on SLES9 (with all graphical devel libs)
>> fails, while linking:
>>
>> gcc -O2 -D__amd64__ -o .libs/aaindexextract aaindexextract.o
>> ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so
>> ../ajax/.libs/libajax.so ../plplot/.libs/libeplplot.so
>> -L/usr/X11R6/lib64
>> /usr/lib64/libgd.so -L/usr/lib64 -lXpm -lX11
>> /usr/lib64/libjpeg.so /usr/lib64/libfreetype.so -lpng12 -lpng -lz -lm
>> -Wl,--rpath -Wl,/usr/local/emboss5/lib
>>
>> ../plplot/.libs/libeplplot.so: undefined reference to `gdImageGifPtr'
>>
>> Configuration:
>> ./configure --prefix=/usr/local/emboss5
>>
>> It seems for me that EMBOSS 5.0.0 is looking for GIF support despite of
>> the fact that newer Versions of
>> gd don't support gif anymore (cf. README line 65).
>>
>> Is there any workarround for the problem (I don't bother changing code)?
>>
>> Best regards
>> Christian
>> --
>> =============================================================================
>> Christian Bolliger
>> IT Services                      | http://www.id.uzh.ch/
>> Central Systems / HPC   	 | http://www.matterhorn.uzh.ch/
>> University of  Zuerich           | E-Mail: christian.bolliger at
>> id.uzh.ch
>> Winterthurerstr. 190             | Tel: +41 (0)1 63 56775
>> CH-8057 Zuerich; Switzerland     | Fax: +41 (0)1 63 54505
>> Mime/S CA:                https://www.ca.unizh.ch/client/
>>
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>
>
>
>
> --------------------------------------------------------------------------------
>
>
> Previous message: [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif
> support
> Next message: [EMBOSS] Sixpack
> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>
> --------------------------------------------------------------------------------
> More information about the EMBOSS mailing list
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>




From zhangcg at bmi.ac.cn  Mon Jul 30 12:07:15 2007
From: zhangcg at bmi.ac.cn (Chenggang Zhang)
Date: Mon, 30 Jul 2007 20:07:15 +0800
Subject: [EMBOSS] EMBOSS 5.0.0 compilation fails on RedHat ver 9.0
	(GDerror)?
References: <200707301537437988523@bmi.ac.cn>,
	<37079.81.98.241.17.1185783773.squirrel@webmail.ebi.ac.uk>
Message-ID: <200707302007137492344@bmi.ac.cn>

Dear Dr. Aln,

Thank you for the kind suggestion. The installation is now OK using the following command:
'./configure --with-pngdriver=/usr/local'

Best regards,

Sincerely yours,
Chenggang Zhang
2007-07-30 20:06:16

==============================================
Chenggang Zhang, PhD, Professor and Director
Department of Neurobiology
Beijing Institute of Radiation Medicine
Taiping Road 27, Beijing, 100850, China.
Tel: +8610-66931590. Fax: +8610-68169574
Cell phone: +8610-13910133213
Email: zhangcg at bmi.ac.cn,  zcgweb at 126.com
       zcgweb at yahoo.com, zcgweb at gmail.com
==============================================

=======Your original message at 2007-07-30 16:23:07=======

>Dear Chenggang Zhang,
>
>There is insufficient detail in your message to be able to answer
>it definitively, except to say that it is a GD error. In general:
>
>1) If the GD update is from RPMs that put the gd and gd-devel
>   files in the standard RH9 system area (unlikely I suppose as
>   RH9 is so old) then you should just do a 'make clean' and
>   './configure' EMBOSS again.
>
>2) If you've compiled gd yourself and the libraries are
>   in (e.g.) /usr/local/lib and the headers under /usr/local/include
>   then, again, 'make clean' but this time add the
>      --with-pngdriver=/usr/local
>   switch to the './configure' line. (Amend /usr/local appropriately
>   if you put the gd files elsewhere).
>
>HTH
>
>Alan
>
>> Dear EMBOSS maintainer,
>>
>> I have the similary question as Christian reported below. However, even if
>> I have updated the GD to version 2.0.28 or 2.0.35, I still failed to
>> install the EMBOSS5 in my computer (uname information: Linux 2.4.20-8smp
>> #1 SMP Thu Mar 13 17:45:54 EST 2003 i686 i686 i386 GNU/Linux, RedHat ver
>> 9.0). The error information was attached below. Could you please tell me
>> how to solve this question?
>>
>> make[2]: Entering directory `/dev/shm/EMBOSS-5.0.0/emboss'
>> /bin/sh ../libtool --tag=CC   --mode=link gcc  -O2   -o aaindexextract
>> aaindexextract.o ../nucleus/libnucleus.la ../ajax/libajaxg.la
>> ../ajax/libajax.la ../plplot/libeplplot.la -L/usr/X11R6/lib -lX11  -lm
>> -lgd
>> -lpng -lz -lm
>> gcc -O2 -o .libs/aaindexextract aaindexextract.o
>> ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so
>> ../ajax/.libs/libajax.so ../plplot/.libs/libeplplot.so -L/usr/X11R6/lib
>> -lX11 -lgd -lpng -lz -lm  -Wl,--rpath -Wl,/usr/local/emboss5/lib
>> ../plplot/.libs/libeplplot.so: undefined reference to `gdImageGifPtr'
>> ../plplot/.libs/libeplplot.so: undefined reference to
>> `gdImageSetThickness'
>> ../plplot/.libs/libeplplot.so: undefined reference to `gdImagePngPtrEx'
>> ../plplot/.libs/libeplplot.so: undefined reference to
>> `gdImageCreateTrueColor'
>> ../plplot/.libs/libeplplot.so: undefined reference to
>> `gdImageSetAntiAliased'
>> collect2: ld returned 1 exit status
>> make[2]: *** [aaindexextract] Error 1
>> make[2]: Leaving directory `/dev/shm/EMBOSS-5.0.0/emboss'
>> make[1]: *** [all-recursive] Error 1
>> make[1]: Leaving directory `/dev/shm/EMBOSS-5.0.0/emboss'
>> make: *** [all-recursive] Error 1
>>
>> Best regards,
>>
>> Sincerely yours,
>> Chenggang Zhang
>> 2007.07.30 15:36:41
>>
>> ==============================================
>> Chenggang Zhang, PhD, Professor and Director
>> Department of Neurobiology
>> Beijing Institute of Radiation Medicine
>> Taiping Road 27, Beijing, 100850, China.
>> Tel: +8610-66931590. Fax: +8610-68169574
>> Cell phone: +8610-13910133213
>> Email: zhangcg at bmi.ac.cn,  zcgweb at 126.com
>>        zcgweb at gmail.com, zcgweb at yahoo.com
>> ==============================================
>>
>>
>>>================================================================================================================
>> [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif support
>> ajb at ebi.ac.uk ajb at ebi.ac.uk
>> Mon Jul 16 12:23:47 EDT 2007
>>
>> Previous message: [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif
>> support
>> Next message: [EMBOSS] Sixpack
>> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>>
>> --------------------------------------------------------------------------------
>>
>> Dear Christian,
>>
>> Support for GIF was restored in gd 2.0.28 on July 21st, 2004. So, as
>> mentioned in the announcement, just install an up-to-date gd2 on SLES 9
>> and the compilation will work.
>>
>> I've updated the development version of README to reflect this.
>>
>> Alan
>>
>>
>>
>>> Dear EMBOSS maintainer
>>>
>>> Compilation of EMBOSS 5.0.0 on SLES9 (with all graphical devel libs)
>>> fails, while linking:
>>>
>>> gcc -O2 -D__amd64__ -o .libs/aaindexextract aaindexextract.o
>>> ../nucleus/.libs/libnucleus.so ../ajax/.libs/libajaxg.so
>>> ../ajax/.libs/libajax.so ../plplot/.libs/libeplplot.so
>>> -L/usr/X11R6/lib64
>>> /usr/lib64/libgd.so -L/usr/lib64 -lXpm -lX11
>>> /usr/lib64/libjpeg.so /usr/lib64/libfreetype.so -lpng12 -lpng -lz -lm
>>> -Wl,--rpath -Wl,/usr/local/emboss5/lib
>>>
>>> ../plplot/.libs/libeplplot.so: undefined reference to `gdImageGifPtr'
>>>
>>> Configuration:
>>> ./configure --prefix=/usr/local/emboss5
>>>
>>> It seems for me that EMBOSS 5.0.0 is looking for GIF support despite of
>>> the fact that newer Versions of
>>> gd don't support gif anymore (cf. README line 65).
>>>
>>> Is there any workarround for the problem (I don't bother changing code)?
>>>
>>> Best regards
>>> Christian
>>> --
>>> =============================================================================
>>> Christian Bolliger
>>> IT Services                      | http://www.id.uzh.ch/
>>> Central Systems / HPC   	 | http://www.matterhorn.uzh.ch/
>>> University of  Zuerich           | E-Mail: christian.bolliger at
>>> id.uzh.ch
>>> Winterthurerstr. 190             | Tel: +41 (0)1 63 56775
>>> CH-8057 Zuerich; Switzerland     | Fax: +41 (0)1 63 54505
>>> Mime/S CA:                https://www.ca.unizh.ch/client/
>>>
>>> _______________________________________________
>>> EMBOSS mailing list
>>> EMBOSS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/emboss
>>>
>>
>>
>>
>>
>> --------------------------------------------------------------------------------
>>
>>
>> Previous message: [EMBOSS] EMBOSS 5.0.0 compilation fails on SLES9 (no gif
>> support
>> Next message: [EMBOSS] Sixpack
>> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>>
>> --------------------------------------------------------------------------------
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>>
>>
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>
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