From gbottu at vub.ac.be Fri Feb 1 11:03:35 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Fri, 01 Feb 2008 17:03:35 +0100 Subject: [EMBOSS] A question about CON entries Message-ID: <47A342D7.1000909@vub.ac.be> Dear friends, As you know, the databanks EMBL, GenBank and RefSeq contain entries that do not contain the sequence itself, but instead "join" information about how to compose the sequence using ranges from other sequences. When the databank has been installed under EMBOSS the sequence is not available, since EMBOSS wil give a "Warning: Sequence has zero length". Do you think that EMBOSS should be able to handle such cases ? And in the meantime, do you know about tools that can, given as input the "CON" sequence and a databank with sequences, assemble on-the-fly the sequence ? Guy Bottu, BEN From pmr at ebi.ac.uk Fri Feb 1 11:55:37 2008 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 01 Feb 2008 16:55:37 +0000 Subject: [EMBOSS] A question about CON entries In-Reply-To: <47A342D7.1000909@vub.ac.be> References: <47A342D7.1000909@vub.ac.be> Message-ID: <47A34F09.8060006@ebi.ac.uk> Guy Bottu wrote: > Dear friends, > > As you know, the databanks EMBL, GenBank and RefSeq contain entries that > do not contain the sequence itself, but instead "join" information about > how to compose the sequence using ranges from other sequences. When the > databank has been installed under EMBOSS the sequence is not available, > since EMBOSS wil give a "Warning: Sequence has zero length". Do you > think that EMBOSS should be able to handle such cases ? And in the > meantime, do you know about tools that can, given as input the "CON" > sequence and a databank with sequences, assemble on-the-fly the sequence ? Yes we need to handle those entries. If you want to request this feature, please tell us. More requests means higher priority :-) When reading a CON entry we need a database to use to read the true sequence and features. If we are reading from a database we can add the information in the database definition. How do we define a default to resolve EMBL CON entries? Can we handle EMBL release and EMBL updates? regards, Peter From gbottu at vub.ac.be Mon Feb 4 04:11:11 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Mon, 04 Feb 2008 10:11:11 +0100 Subject: [EMBOSS] A question about CON entries In-Reply-To: <47A34F09.8060006@ebi.ac.uk> References: <47A342D7.1000909@vub.ac.be> <47A34F09.8060006@ebi.ac.uk> Message-ID: <47A6D6AF.7080802@vub.ac.be> Peter Rice wrote: > When reading a CON entry we need a database to use to read the true > sequence and features. > > If we are reading from a database we can add the information in the > database definition. > > How do we define a default to resolve EMBL CON entries? > > Can we handle EMBL release and EMBL updates? There are a number of practical issues : - an entry with "join" information can come from a databank as well as from a file. - EMBL and GenBank CON entries refer to segments in the same databank, but RefSeq refers to GenBank. - a sequence presented to EMBOSS can be CON or ANN type but have already a re-assembled sequence (depending on where it comes from) - each site has its own DB entries in emboss.default, so code that explicitly says "search in embl" might not work So, IMHO : - We need code for two cases : embl format (for EMBL,...) and for GenBank format (for GenBank, RefSeq,...). The software must look whether there are CO respectively CONTIG lines in the entry, looking for CON in the ID line is not good. - for databank sequences : the DB entry in emboss.default should have a parameter that indicates in which databank to search for the segments. If a site has RefSeq and EMBL but no GenBank, then RefSeq could still use sequence information from EMBL. If there is no parameter in the DB entry EMBOSS could for embl or genbank format entries search by default in the same databank or simply not try the assembly (what do you think is the best ?). - for "personal" sequences from files : is more tricky. Maybe an associated or advanced parameter that says that if the input sequence is of "join" type it must use a databank or file to retrieve the sequences. E.g. -sjoin=xxx or -join=xxx. If xxx is a databank the seqgments can be retrieved using the standard method defined in emboss.default and if xxx is a file it can be searched sequentially. There are still some issues : - the program entret is for retrieving entries as they are rather then for processing sequence information. Should entret also try the assembly or not ? - feature information is another matter. Some entries have no or a very poor feature information but there are entries that have features that are different from the seqment entries (this is certainly so for the ANN entries in EMBL and for RefSeq). How should we handle this ? Guy Bottu, BEN From rls at ebi.ac.uk Mon Feb 4 04:57:00 2008 From: rls at ebi.ac.uk (Rodrigo Lopez) Date: Mon, 04 Feb 2008 09:57:00 +0000 Subject: [EMBOSS] A question about CON entries In-Reply-To: <47A6D6AF.7080802@vub.ac.be> References: <47A342D7.1000909@vub.ac.be> <47A34F09.8060006@ebi.ac.uk> <47A6D6AF.7080802@vub.ac.be> Message-ID: <47A6E16C.3050904@ebi.ac.uk> Hi, In the context of this thread I think it is worth pointing out that the CON entries in EMBL exist in expanded form (i.e. with the sequence) on the EBI ftp server in the following forms: EMBL CONTIGS EXPANDED ftp://ftp.ebi.ac.uk/pub/databases/embl/expanded_con EMBL ANNOTATED CON ftp://ftp/ebi.ac.uk/pub/databases/embl/annotated_con For comments and suggestions regarding these entries please contact: http://www.ebi.ac.uk/embl/Contact/ http://www.ebi.ac.uk/support/ - SUe subject 'EMBL' R:) Guy Bottu wrote: > Peter Rice wrote: >> When reading a CON entry we need a database to use to read the true >> sequence and features. >> >> If we are reading from a database we can add the information in the >> database definition. >> >> How do we define a default to resolve EMBL CON entries? >> >> Can we handle EMBL release and EMBL updates? > > There are a number of practical issues : > - an entry with "join" information can come from a databank as well as > from a file. > - EMBL and GenBank CON entries refer to segments in the same databank, > but RefSeq refers to GenBank. > - a sequence presented to EMBOSS can be CON or ANN type but have already > a re-assembled sequence (depending on where it comes from) > - each site has its own DB entries in emboss.default, so code that > explicitly says "search in embl" might not work > > So, IMHO : > - We need code for two cases : embl format (for EMBL,...) and for > GenBank format (for GenBank, RefSeq,...). The software must look whether > there are CO respectively CONTIG lines in the entry, looking for CON in > the ID line is not good. > - for databank sequences : the DB entry in emboss.default should have a > parameter that indicates in which databank to search for the segments. > If a site has RefSeq and EMBL but no GenBank, then RefSeq could still > use sequence information from EMBL. If there is no parameter in the DB > entry EMBOSS could for embl or genbank format entries search by default > in the same databank or simply not try the assembly (what do you think > is the best ?). > - for "personal" sequences from files : is more tricky. Maybe an > associated or advanced parameter that says that if the input sequence is > of "join" type it must use a databank or file to retrieve the sequences. > E.g. -sjoin=xxx or -join=xxx. If xxx is a databank the seqgments can be > retrieved using the standard method defined in emboss.default and if > xxx is a file it can be searched sequentially. > > There are still some issues : > - the program entret is for retrieving entries as they are rather then > for processing sequence information. Should entret also try the assembly > or not ? > - feature information is another matter. Some entries have no or a very > poor feature information but there are entries that have features that > are different from the seqment entries (this is certainly so for the ANN > entries in EMBL and for RefSeq). How should we handle this ? > > > Guy Bottu, > BEN > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From jeedward at yahoo.com Wed Feb 6 10:54:58 2008 From: jeedward at yahoo.com (John Edward) Date: Wed, 6 Feb 2008 07:54:58 -0800 (PST) Subject: [EMBOSS] Draft paper submission deadline is extended: BCBGC-08 Message-ID: <156631.69309.qm@web45904.mail.sp1.yahoo.com> Dear Professors, Colleagues and Friends Kindly share the announcement below with those who may be interested: thank you in advance. Sincerely John Edward BCBGC-08 Draft paper submission deadline is extended. The 2008 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) (website: www.PromoteResearch.org ) will be held during July 7-10 2008 in Orlando, FL, USA. The draft paper submission deadline is extended until February 19 2008 due to several requests from the authors. The conference will be held at the same time and location where several major events (see below) will be taking place. BCBGC brings together both academic and industrial scientists and developers from a diverse range of disciplines including bioinformatics, computer science, computational biology, genomics, proteomics and chemoinformatics. One of the main goals of the conference is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers in different fields. Papers that demonstrate applications of existing techniques or developments of new methods are equally welcomed to the conference. Sincerely John Edward ? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-08) ? International Conference on Automation, Robotics and Control Systems (ARCS-08) ? International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) ? International Conference on Enterprise Information Systems and Web Technologies (EISWT-08) ? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-08) ? International Conference on Software Engineering Theory and Practice (SETP-08) ? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-08) --------------------------------- Never miss a thing. Make Yahoo your homepage. From staffa at niehs.nih.gov Thu Feb 7 13:41:10 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Thu, 07 Feb 2008 13:41:10 -0500 Subject: [EMBOSS] Fasta Message-ID: ?There's no fasta in EMBOSS????? We have the latest EMBOSS and we now got Jemboss to run. I don't see fasta. Nick Staffa Telephone: 919-316-4569 (NIEHS: 6-4569) Scientific Computing Support Group NIEHS Information Technology Support Services Contract (Science Task Monitor: Roy W. Reter (reter at niehs.nih.gov) National Institute of Environmental Health Sciences National Institutes of Health Research Triangle Park, North Carolina From gbottu at vub.ac.be Fri Feb 8 11:57:33 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Fri, 08 Feb 2008 17:57:33 +0100 Subject: [EMBOSS] Fasta In-Reply-To: References: Message-ID: <47AC89FD.3020405@vub.ac.be> Staffa, Nick (NIH/NIEHS) wrote: > ?There's no fasta in EMBOSS????? > We have the latest EMBOSS and we now got Jemboss to run. > I don't see fasta. GCG had a GCGized version of fastA but there never was a fastA in EMBOSS. You can however install the native fastA from U. Virginia and put on top of it wrappers4EMBOSS (http://wemboss.sourceforge.net/). I do not know how easy or difficult it is to make it run properly under Jemboss ; if you try, let us all know. Regards, Guy Bottu, Belgian EMBnet Node From shrish at ccmb.res.in Mon Feb 11 01:02:43 2008 From: shrish at ccmb.res.in (Shrish Tiwari) Date: Mon, 11 Feb 2008 11:32:43 +0530 (IST) Subject: [EMBOSS] finding genes/features in flanks of region of interest Message-ID: <4652122.1202709763711.JavaMail.root@127.0.0.1> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From staffa at niehs.nih.gov Mon Feb 11 16:49:06 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Mon, 11 Feb 2008 16:49:06 -0500 Subject: [EMBOSS] Jemboss Guide Message-ID: We are trying to get Emboss/Jemboss up and smoothly running here. We have installed them on a Unix server. In doing what it says in the Jemboss Guide section named Practical, I don't get the program output for Wossname or Showdb. All I get is a window named Saved Results, which shows the command line generated. It's just wonderful that I can choose my font size and Plain/Bold/Italic for this window. Help! Where's my output? Nick Staffa Telephone: 919-316-4569 (NIEHS: 6-4569) Scientific Computing Support Group NIEHS Information Technology Support Services Contract (Science Task Monitor: Roy W. Reter (reter at niehs.nih.gov) National Institute of Environmental Health Sciences National Institutes of Health Research Triangle Park, North Carolina From jeedward at yahoo.com Mon Feb 11 22:08:20 2008 From: jeedward at yahoo.com (John Edward) Date: Mon, 11 Feb 2008 19:08:20 -0800 (PST) Subject: [EMBOSS] BCBGC-08 Draft paper submission deadline is just few days from now Message-ID: <563574.18933.qm@web45915.mail.sp1.yahoo.com> Dear Professors, Colleagues and Friends Kindly share the announcement below with those who may be interested: thank you in advance. Sincerely John Edward BCBGC-08 Draft paper submission deadline is just few days from now The 2008 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) (website: www.PromoteResearch.org ) will be held during July 7-10 2008 in Orlando, FL, USA. The draft paper submission deadline is extended until February 19 2008 due to several requests from the authors. The conference will be held at the same time and location where several major events (see below) will be taking place. BCBGC brings together both academic and industrial scientists and developers from a diverse range of disciplines including bioinformatics, computer science, computational biology, genomics, proteomics and chemoinformatics. One of the main goals of the conference is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers in different fields. Papers that demonstrate applications of existing techniques or developments of new methods are equally welcomed to the conference. Sincerely John Edward ? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-08) ? International Conference on Automation, Robotics and Control Systems (ARCS-08) ? International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) ? International Conference on Enterprise Information Systems and Web Technologies (EISWT-08) ? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-08) ? International Conference on Software Engineering Theory and Practice (SETP-08) ? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-08) --------------------------------- Never miss a thing. Make Yahoo your homepage. From ajb at ebi.ac.uk Tue Feb 12 09:32:51 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 12 Feb 2008 14:32:51 -0000 (GMT) Subject: [EMBOSS] Jemboss Guide In-Reply-To: References: Message-ID: <37056.86.14.232.77.1202826771.squirrel@webmail.ebi.ac.uk> The first thing to check is whether the programs work from the command line. That will show whether any library dependencies are missing. Remember that the installed EMBOSS applications 'bin' directory must be in your PATH for wossname to work properly from the command line. The second thing to check is that the jembossctl application has been properly made suid root e.g.: -rwsr-xr-x 1 root users 44380 2008-02-09 11:11 jembossctl If you installed Jemboss without using the installation script (we recommend that you do use the script) then you should also check your jemboss.properties file carefully. That lives in .../share/EMBOSS/jemboss/resources and will look something like this for an installation in /usr/local/emboss with SSL authentication activated: user.auth=true jemboss.server=true server.public=https://1.2.3.4:8443/axis/services server.private=https://1.2.3.4:8443/axis/services service.public=JembossAuthServer service.private=JembossAuthServer plplot=/usr/local/emboss/share/EMBOSS/ embossData=/usr/local/emboss/share/EMBOSS/data/ embossBin=/usr/local/emboss/bin/ embossPath=/usr/bin/:/bin:/usr/local/bin acdDirToParse=/usr/local/emboss/share/EMBOSS/acd/ embossURL=http://emboss.sourceforge.net/ > All I get is a window named Saved Results, which shows the command line > generated. It's just wonderful that I can choose my font size and > Plain/Bold/Italic for this window. Thank you. Alan From andi_amare at yahoo.com Tue Feb 12 17:13:43 2008 From: andi_amare at yahoo.com (andinet amare) Date: Tue, 12 Feb 2008 14:13:43 -0800 (PST) Subject: [EMBOSS] configuring mEMBOSS Message-ID: <112429.34658.qm@web35906.mail.mud.yahoo.com> Hi, I am new to EMBOSS and Unix. I installed cygwin and mEMBOSS 5.0. When I try to configure mEmboss with ./configure, I get a message that says 'bash: ./configure: No such file or directory.' And I don't see a 'configure.exe' file with ls command. I appreciate any help. I am following the instructions from: http://emboss.open-bio.org/pipermail/emboss/2006-May/002537.html' Thanks Andinet --------------------------------- Never miss a thing. Make Yahoo your homepage. From uludag at ebi.ac.uk Wed Feb 13 09:04:19 2008 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Wed, 13 Feb 2008 14:04:19 +0000 Subject: [EMBOSS] configuring mEMBOSS In-Reply-To: <112429.34658.qm@web35906.mail.mud.yahoo.com> References: <112429.34658.qm@web35906.mail.mud.yahoo.com> Message-ID: <1202911459.13491.60.camel@emboss2.ebi.ac.uk> Hi, > I am new to EMBOSS and Unix. I installed cygwin and mEMBOSS 5.0. When I try to configure mEmboss with ./configure, I get a message that says 'bash: ./configure: No such file or directory.' And I don't see a 'configure.exe' file with ls command. I appreciate any help. > > I am following the instructions from: > http://emboss.open-bio.org/pipermail/emboss/2006-May/002537.html' I think you should not use cygwin. The instructions above should probably was for installing the standard version before mEMBOSS was developed. I guess mEMBOSS should directly be installed. Possibly by executing the file you downloaded, which should be the following. ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-5.0.0-setup.exe I noticed there is a readme file as well. ftp://emboss.open-bio.org/pub/EMBOSS/windows/README.win Regards, Mahmut From jison at ebi.ac.uk Fri Feb 15 08:58:21 2008 From: jison at ebi.ac.uk (Jon Ison) Date: Fri, 15 Feb 2008 13:58:21 -0000 (GMT) Subject: [EMBOSS] finding genes/features in flanks of region of interest In-Reply-To: <4652122.1202709763711.JavaMail.root@127.0.0.1> References: <4652122.1202709763711.JavaMail.root@127.0.0.1> Message-ID: <59985.84.92.187.247.1203083901.squirrel@webmail.ebi.ac.uk> Hi Shrish As a starting point, you could have a look at getorf: http://emboss.sourceforge.net/apps/cvs/emboss/apps/getorf.html which will (optionally) return regions flanking START and / or STOP codons. If you know an exact region of interest that can be specified with -sbegin and -send for any input sequence. Cheers Jon > Hi! > Does anyone know how to find genes in sequences flanking a region of interest? Most programs require the length of > flanks to scan. We are interested in the nearest genes on either side, and maybe the distance of the gene to our > region of interest. > Shrish > Dr. Shrish Tiwari > E503, Centre for Cellular and Molecular Biology > Uppal Road, Hyderabad - 500 007, INDIA > Phone: 91-40-27192777 > Alternate email: shrish.geo at yahoo.com > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From siegmund at develogen.com Wed Feb 20 03:49:25 2008 From: siegmund at develogen.com (Thomas Siegmund) Date: Wed, 20 Feb 2008 09:49:25 +0100 Subject: [EMBOSS] Kaptain GUI for EMBOSS 5.0 Message-ID: <200802200949.26692.siegmund@develogen.com> Dear list, I'm happy to announce a new version of the Kaptain user interface for EMBOSS. EMBOSS.kaptain v.0.98 provides a simple and efficient GUI to use EMBOSS 5.0 and the embossified Phylip 3.6b on the desktop. The GUI depends on Kaptain, a tool to build nice graphical user interfaces for command line applications like EMBOSS. Kaptain is a Qt3 application. Due to problems with it's configure script it got more and more difficult to install on recent systems. To address this, and to make Kaptain a little more future-proof I have ported it to the modern cMake build system and to Qt4. A patch and build instructions are in the EMBOSS.kaptn package. You can find the package, some screenshots, and additional information as usual here: http://userpage.fu-berlin.de/~sgmd/download.html For Mac users Koen van der Drift provides a fink package at: http://pdb.finkproject.org/pdb/package.php/emboss-kaptain Qt4 is availible under various open source licenses for Windows as well. Thus with Kaptain on Qt4 it may be possible to build and use the Kaptain GUI on that OS as well. Have fun Thomas -- Dr. Thomas Siegmund DeveloGen AG Manager Bioinformatics Phone: +49(551) 505 58 651 http://www.develogen.com From Johanne.Duhaime at ircm.qc.ca Tue Feb 26 14:52:13 2008 From: Johanne.Duhaime at ircm.qc.ca (Duhaime Johanne) Date: Tue, 26 Feb 2008 14:52:13 -0500 Subject: [EMBOSS] EmbossExplorer : problem to install Message-ID: Hello This message have also been directed to sourceForge. But I did not have any answer for now. Is there someone in this list can help me? I have tried to install EmbossExplorer but I keep having the following message: The requested URL /cgi-bin/emboss/intro was not found on this server when I tried to access the site. /cgi-bin/emboss/intro is not there for sure as you could see below where I have put the installation process and the file created. I have other application cgi/perl running well on that server. I have seen a mail where someone has the same problem but there was no solution as far as I have seen. Here is the installation view: ./install installing EMBOSS Explorer perl modules... Writing Makefile for EMBOSS::GUI Manifying blib/man3/EMBOSS::GUI.3 Manifying blib/man3/EMBOSS::ACD.3 Manifying blib/man3/EMBOSS::GUI::Conf.3 Manifying blib/man3/EMBOSS::GUI::XHTML.3 Manifying blib/man3/EMBOSS::GUI.3 Manifying blib/man3/EMBOSS::ACD.3 Manifying blib/man3/EMBOSS::GUI::Conf.3 Manifying blib/man3/EMBOSS::GUI::XHTML.3 Installing /usr/local/lib/perl5/site_perl/5.8.5/EMBOSS/GUI/Conf.pm Writing /usr/local/lib/perl5/site_perl/5.8.5/sun4-solaris/auto/EMBOSS/GUI/.packlist Appending installation info to /usr/local/lib/perl5/5.8.5/sun4-solaris/perllocal.pod `install' is up to date. installing EMBOSS Explorer GUI components... I need to collect some information in order to install EMBOSS Explorer: ./install: embossversion: not found -e Where was EMBOSS installed? (default is /usr/local) /home/sasircm/emboss/EMBOSS5bin/ -e Where should the EMBOSS Explorer HTML files be installed? (default is /var/www/html/emboss) /opt/apache/htdocs/emboss -e What is the URL prefix corresponding to the HTML directory above? (default is /emboss) -e Where should the EMBOSS Explorer CGI script be installed? (default is /var/www/cgi-bin/emboss) /opt/apache/cgi-bin/emboss -e What is the complete URL corresponding to the CGI script '/opt/apache/cgi-bin/emboss/emboss'? (default is /cgi-bin/emboss) installing HTML files to /opt/apache/htdocs/emboss... creating HTML index file at /opt/apache/htdocs/emboss/index.html... creating output directory at /opt/apache/htdocs/emboss/output... installing CGI script to /opt/apache/cgi-bin/emboss/emboss... copying manual support files to /opt/apache/htdocs/emboss/manual... fixing permissions... EMBOSS Explorer is installed. Visit /cgi-bin/emboss to test it out. Site configuration (including a list of applications to be excluded from public access) is stored in the EMBOSS::GUI::Conf module (located at /usr/local/lib/perl5/site_perl/5.8.5/EMBOSS/GUI/Conf.pm). The main style sheet, which can be edited to customize the appearance of EMBOSS Explorer is /opt/apache/htdocs/emboss/style/emboss.css. If you prefer the look and feel of the old EMBOSS GUI, you can use /opt/apache/htdocs/emboss/style/classic.css instead (the style sheet is specified in the EMBOSS::GUI::Conf module). EMBOSS Explorer generates temporary output files every time an application is used. Depending on the tasks being performed, these output files can consume space fairly quickly. The old output can be cleaned up on a regular basis by adding a task to the root user's crontab. The following example runs every morning at 0400 and removes all output files that have not been accessed in the last 24 hours: 0 4 * * * find /opt/apache/htdocs/emboss/output -type d -mindepth 1 -maxdepth 1 -atime 1 -exec rm -rf {} \; Please report any errors or strange occurrences using the bug tracker at http://sourceforge.net/tracker/?func=add&group_id=124389&atid=699414 ----------------------------------------------- Here are the web directories /opt/apache/htdocs/emboss images/ index.html manual/ output/ style/ /opt/apache/cgi-bin/emboss/ emboss* -------------------------------------------------- emboss-explorer-2.2.0.tar.gz solaris 5.9 perl v5.8.5 EMBOSS-5.0.0.tar.gz Thank you in advance Johanne Duhaime duhaimj at ircm.qc.ca tel 5556 local 1565.4, Centre de documentation From david.bauer at bayerhealthcare.com Thu Feb 28 04:01:50 2008 From: david.bauer at bayerhealthcare.com (david.bauer at bayerhealthcare.com) Date: Thu, 28 Feb 2008 10:01:50 +0100 Subject: [EMBOSS] EmbossExplorer : problem to install In-Reply-To: Message-ID: Hi Johanne, emboss-bounces at lists.open-bio.org schrieb am 26/02/2008 20:52:13: > The requested URL /cgi-bin/emboss/intro was not found on this server > when I tried to access the site. > > /cgi-bin/emboss/intro is not there for sure as you could see below > where I have put the installation process and the file created. I have no idea what this means. According to what you specified during installtion there should be a start script "emboss" in /opt/apache/cgi-bin/emboss So the starting url would be http://yourserver/cgi-bin/emboss/emboss > I need to collect some information in order to install EMBOSS Explorer: > ./install: embossversion: not found > -e Where was EMBOSS installed? > (default is /usr/local) > /home/sasircm/emboss/EMBOSS5bin/ It looks like this is the directory just with the binaries and with non standard name. So this could cause problems. Check all the path variables defined in /usr/local/lib/perl5/site_perl/5.8.5/EMBOSS/GUI/Conf.pm and adjust them according to you directory structure of the emboss installation. Hope this helps, David.