From cbonnard at isrec-sg1.unil.ch Tue Jan 7 03:10:17 2003 From: cbonnard at isrec-sg1.unil.ch (Claude Bonnard) Date: Tue, 7 Jan 2003 09:10:17 +0100 Subject: systematic error message Message-ID: <10301070910.ZM27222@isrec-sg1> Hello, I have a message which shows up with every emboss program and I do not find where it is coming from. does someone have a clue? of more fenerally a method for such problems? the "-debug" swithc does not show any indication of the problem in the .dbg file. the current emboss.default looks ok (?) the message is : Error: Bad database attribute '' after that, the program runs as expected... Thanks for your help regards Claude -- Claude Bonnard Ph.D. ISREC (Swiss Institute for Experimental Cancer Research) Bioinformatics Group Ch des Boveresses 155 CH-1066 Epalinges Switzerland phone: [41-21]-692-5891 fax: [41-21]-652-6933 From pmr at ebi.ac.uk Tue Jan 7 04:40:16 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 07 Jan 2003 09:40:16 +0000 Subject: systematic error message References: <10301070910.ZM27222@isrec-sg1> Message-ID: <3E1AA080.E174CB88@ebi.ac.uk> Hi Claude, > Error: Bad database attribute '' > > after that, the program runs as expected... Somewhere in emboss.defaults (or .embossrc) you have a bad database definition. Most probably in the last change you made there. I will look into adding the database name to the error message to help find it in fiture releases. Also, maybe this should be a really fatal error... regards, Peter (now at EBI) From asen.nenov at metalife.de Thu Jan 9 02:40:48 2003 From: asen.nenov at metalife.de (Asen Nenov) Date: Thu, 9 Jan 2003 09:40:48 +0200 Subject: Sixpack missing Message-ID: <003e01c2b7b2$75338e90$3801a8c0@metalife.bg> Hello, I was trying to run Sixpackon my server after downloading EMBOSS 2.5.1. Unfortunately it does'n happened to be in the distribution. Could anyone have an explanation for this problem? [or it's just me ;-)] Any help appreciated. Regards Asen Nenov METALIFE AG - Sofia, Bulgaria asen.nenov at metalife.de www.metalife.de ++359 2 950 1802 From stefanielager at fastmail.ca Thu Jan 9 03:14:57 2003 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Thu, 9 Jan 2003 03:14:57 -0500 (EST) Subject: Sixpack missing Message-ID: <3E1D2F81.0000A1.96511@ns.interchange.ca> Sixpack PROBABLY belong to the new programs (Written (November 2002) - Thomas Laurent) which is due in the NEXT release. There are some other programs with the same status , like sirna. Stefanie > Hello, > > I was trying to run Sixpackon my server after downloading EMBOSS > 2.5.1. Unfortunately it does'n happened to be in the distribution. > Could anyone have an explanation for this problem? [or it's just > me ;-)] Any help appreciated. > > Regards > Asen Nenov > > METALIFE AG - Sofia, Bulgaria > asen.nenov at metalife.de > www.metalife.de > ++359 2 950 1802 _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From ruediger at sanbi.ac.za Fri Jan 10 05:11:47 2003 From: ruediger at sanbi.ac.za (Ruediger Braeuning) Date: Fri, 10 Jan 2003 12:11:47 +0200 (SAST) Subject: Schedule for new EMBOSS release Message-ID: <20030110121048.T6479-100000@fling.sanbi.ac.za> Hi everybody, I was wondering if a new release of EMBOSS is scheduled for the next days? Thanks Ruediger ------------------------------------------------------------------------- Ruediger Braeuning / South African National Bioinformatics Institute (=) University of the Western Cape Ph. +27 21 959 3645 / Private Bag X17 Fax +27 21 959 2512 (=) Bellville, 7535 www.sanbi.ac.za / South Africa From ableasby at hgmp.mrc.ac.uk Fri Jan 10 05:18:19 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 10 Jan 2003 10:18:19 GMT Subject: Schedule for new EMBOSS release Message-ID: <200301101018.KAA21210@bromine.hgmp.mrc.ac.uk> There will be a release soon. As has been pointed out on the group there have been a few new programs added. Alan From areagp61 at yahoo.it Fri Jan 10 08:30:37 2003 From: areagp61 at yahoo.it (Graziano P.) Date: Fri, 10 Jan 2003 14:30:37 +0100 Subject: seqretsplit Message-ID: <000c01c2b8ac$810e9f20$68b6ccc1@biologia.uniba.it> Hi all, I have a single file containing 164 sequences in embl format retrieved by SRS. I want to split all the entries in distinct files. I have tried to use "seqretsplit", but it do not report FT lines. For example: My entry retrieved by means of SRS is: ID AY045754_4; parent: AY045754AC AY045754; FT rRNA 610. .772 FT /product="5.8S ribosomal RNA" SQ Sequence 163 BP; TATATTCTAG CCTTATCGGT GGATCACTCG GCTCGTGGAT CGATGAAGAA CGCAGCCAAC 60 TGCGATAATT AGTGTGAACT GCAGAAACCT TGAACACTGA ACTTTCGAAT GCACATTGCG 120 CCATTGGAGT TATATCCATT GCACGCCTGG TTCAGGGTCG TAA 163 // but seqretsplit convert it in: ID AY045754_4 standard; DNA; UNC; 163 BP. SQ Sequence 163 BP; 43 A; 37 C; 39 G; 44 T; 0 other; TATATTCTAG CCTTATCGGT GGATCACTCG GCTCGTGGAT CGATGAAGAA CGCAGCCAAC 6 TGCGATAATT AGTGTGAACT GCAGAAACCT TGAACACTGA ACTTTCGAAT GCACATTGCG 12 CCATTGGAGT TATATCCATT GCACGCCTGG TTCAGGGTCG TAA 16 // Anyone knows an application or a script that allows me to split sequences (embl format) in different files without losing FT lines? Best regards Graziano -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20030110/952875b3/attachment.html From pmr at ebi.ac.uk Fri Jan 10 09:36:53 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 10 Jan 2003 14:36:53 +0000 Subject: seqretsplit References: <000c01c2b8ac$810e9f20$68b6ccc1@biologia.uniba.it> Message-ID: <3E1EDA85.4080106@ebi.ac.uk> Ciao Graziono, > I have a single file containing 164 sequences in embl format > retrieved by SRS. I want to split all the entries in distinct files. I > have tried to use "seqretsplit", but it do not report FT lines. For example: > My entry retrieved by means of SRS is: > > ID AY045754_4; parent: AY045754AC AY045754; > FT rRNA 610. .772 > FT /product="5.8S ribosomal RNA" This must be a GCG format database, indexed in SRS ... you have gaps in the ".." format. Ideally SRS would fix that ... but EMBOSS could cope with some small changes. Anyway, an SRS fix is non-trivial because it is reporting exactly the text that GCG stores. > Anyone knows an application or a script that allows me to split > sequences (embl format) in different files without losing FT lines? Simplest in your case would be a script that changes ". ." to ".." before passing the data to EMBOSS. Meanwhile, I will take a look at fixing this for a future release. regards, Peter From kim at inb.uni-luebeck.de Tue Jan 14 11:07:19 2003 From: kim at inb.uni-luebeck.de (Jan T. Kim) Date: Tue, 14 Jan 2003 17:07:19 +0100 Subject: Nucleotide profiles with prophecy and profit? Message-ID: <20030114170719.C21341@pc10.inb.mu-luebeck.de> Dear EMBOSSers, we have recently attempted to use the programs prophecy and profit with nucleotide sequences, but we could not figure out how to do this. It appears that the prophecy program unconditionally assumes amino acid sequences -- even converting the FASTA formatted file to msf format and verifying that it says "Type: N" in that, prophecy insists on outputting a x 20 matrix instead of a x 4 one. It was also not possible to convince profit to accept a hand-written x 4 matrix. Could anyone point out to me how to proceed for search nucleotide sequences with a profile matrix? I have noticed the tfscan program, but it seems that employing this would require to construct some kind of mock-up TRANSFAC around my matrix just so I can scan sequences with that. Probably, I have overlooked the obvious and now started to think of twisted ways to do such a scan...? Thanks in advance for your help. Greetinx, Jan -- +- Jan T. Kim -------------------------------------------------------+ | *NEW* email: kim at inb.uni-luebeck.de | | *NEW* WWW: http://www.inb.uni-luebeck.de/staff/kim.html | *-----=< hierarchical systems are for files, not for humans >=-----* From p.ernst at dkfz-heidelberg.de Tue Jan 14 12:15:29 2003 From: p.ernst at dkfz-heidelberg.de (Peter Ernst) Date: Tue, 14 Jan 2003 18:15:29 +0100 (MET) Subject: Perl Module Bio-Emboss-0.1 released Message-ID: Hello, this is an announcement of the first test release of Bio::Emboss perl module version 0.1 =================================== This module interfaces to the libraries of the EMBOSS package. With this module you can access EMBOSS databases and use EMBOSS functions to manipulate data. You can write perl programs that look like any other EMBOSS program (command-line, web interface). SYNOPSIS use Bio::Emboss qw(:all); embInitPerl("seqret", \@ARGV); $seqall = ajAcdGetSeqall("sequence"); $seqout = ajAcdGetSeqoutall("outseq"); $firstonly = ajAcdGetBool ("firstonly"); while ($seqall->ajSeqallNext($seq)) { $seqout->ajSeqAllWrite ($seq); last if $firstonly; } DOWNLOAD ftp://genome.dkfz-heidelberg.de/pub/emboss/perl/ and CPAN (soon) REQUIREMENTS EMBOSS-2.5.1 (including sources) (I don't know if it will work with earlier versions.) STATUS There are interfaces to most (but not all) functions in libajax. There are only a few interfaces to functions in libnucleus. Most functions have *not* been tested yet (Emboss is big !), however a few test scripts are provided. AUTHOR Peter Ernst, -- ======================================================================= Peter Ernst Department of Molecular Biophysics - B020 Deutsches Krebsforschungszentrum (German Cancer Research Center) DKFZ Im Neuenheimer Feld 580 / Technologiepark 3 69120 Heidelberg, Germany phone: +49-6221-42-2330 http://genome.dkfz-heidelberg.de/ fax: +49-6221-42-2333 ======================================================================= From kellert at ohsu.edu Tue Jan 14 18:31:35 2003 From: kellert at ohsu.edu (Thomas Keller) Date: Tue, 14 Jan 2003 15:31:35 -0800 Subject: EMBOSS: abiview Message-ID: <5217F7D9-2818-11D7-8AB5-0003930405E2@ohsu.edu> Greetings, I'm a new EMBOSS user, so please be gentle. I'm using my local installation on a Mac running OS 10.2.1. "abiview": four color plot is generated, but -window option allows more bases, but how does one view for example bases 200-250? My home directory .embossrc file looks like this: # EMBOSS configuration file for kellert set emboss_acdroot /usr/local/biotools/share/EMBOSS/acd set emboss_database_dir /usr/local/biotools/data/dbs I source a file containing the following env variables when I launch a terminal or xterm window: set path=(/usr/local/biotools/bin $path) setenv MANPATH ${MANPATH}:/usr/local/biotools/man setenv WISECONFIGDIR /usr/local/biotools/wisecfg/ setenv EMBOSS_ACDROOT /usr/local/biotools/share/EMBOSS/acd setenv EMBOSS_DATA /usr/local/biotools/share/EMBOSS/data setenv PLPLOT_LIB /usr/local/biotools/share/EMBOSS Thanks, Tom K. Thomas J. Keller, Ph.D. Oregon Health & Science University MMI Research Core Facility 3181 SW Sam Jackson Park Rd. Portland, OR, USA, 97239 http://www.ohsu.edu/core -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1109 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20030114/12cabc93/attachment.bin From newgene at bigfoot.com Tue Jan 14 21:29:11 2003 From: newgene at bigfoot.com (clwu) Date: Tue, 14 Jan 2003 20:29:11 -0600 Subject: Q on "diffseq" Message-ID: <3E24C777.8030808@bigfoot.com> Hi, Group, I have one copy of EMBOSS (ver2.5.1) installed locally under cygwin/win2k. I expected "diffseq" can do the job as its name. However, I found it can not identify the different sequence at the both ends of input sequences. Only the different seq. inside can be indentified. Why? Is it the design purpose? How can I get all different sequences I need? Thank you. Chunlei From grsvc at mucc.mahidol.ac.th Tue Jan 14 22:57:40 2003 From: grsvc at mucc.mahidol.ac.th (Suksiri Vichasri Grams) Date: Wed, 15 Jan 2003 10:57:40 +0700 Subject: EMBOSS: abiview In-Reply-To: <5217F7D9-2818-11D7-8AB5-0003930405E2@ohsu.edu> Message-ID: <7E095164-283D-11D7-9826-000393629C54@mucc.mahidol.ac.th> Hi, abiview has two options named -startbase and -endbase which can be used to limit the analysis to the entered values. Kindly, Rudi On Wednesday, Jan 15, 2003, at 06:31 Asia/Jakarta, Thomas Keller wrote: > Greetings, > I'm a new EMBOSS user, so please be gentle. > I'm using my local installation on a Mac running OS 10.2.1. > "abiview": four color plot is generated, but -window option allows > more bases, but how does one view for example bases 200-250? > My home directory .embossrc file looks like this: > # EMBOSS configuration file for kellert > set emboss_acdroot /usr/local/biotools/share/EMBOSS/acd > set emboss_database_dir /usr/local/biotools/data/dbs > > I source a file containing the following env variables when I launch a > terminal or xterm window: > set path=(/usr/local/biotools/bin $path) > setenv MANPATH ${MANPATH}:/usr/local/biotools/man > setenv WISECONFIGDIR /usr/local/biotools/wisecfg/ > setenv EMBOSS_ACDROOT /usr/local/biotools/share/EMBOSS/acd > setenv EMBOSS_DATA /usr/local/biotools/share/EMBOSS/data > setenv PLPLOT_LIB /usr/local/biotools/share/EMBOSS > > Thanks, > Tom K. > > Thomas J. Keller, Ph.D. > Oregon Health & Science University > MMI Research Core Facility > 3181 SW Sam Jackson Park Rd. > Portland, OR, USA, 97239 > > http://www.ohsu.edu/core > From stefanielager at fastmail.ca Wed Jan 15 02:44:58 2003 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Wed, 15 Jan 2003 02:44:58 -0500 (EST) Subject: Q on Message-ID: <3E25117A.000081.16653@ns.interchange.ca> diffseq use a local wordmatch alignment algorithm, it finds gaps but at the ends you can't match against NOTHING. Try using a global alignment algorithm instead (e.g. needle or stretcher). But maybe it could be an option in diffseq to use either use a local or global alignment algorithm? Stefanie > Hi, Group, > I have one copy of EMBOSS (ver2.5.1) installed locally under > cygwin/win2k. I expected "diffseq" can do the job as its name. > However, I found it can not identify the different sequence at the > both ends of input sequences. Only the different seq. inside can > be indentified. Why? Is it the design purpose? How can I get all > different sequences I need? > > Thank you. > > Chunlei > > _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From newgene at bigfoot.com Wed Jan 15 13:38:07 2003 From: newgene at bigfoot.com (clwu) Date: Wed, 15 Jan 2003 12:38:07 -0600 Subject: Q on References: <3E25117A.000081.16653@ns.interchange.ca> Message-ID: <3E25AA8F.4030304@bigfoot.com> Thank you, Stefanie. I can get the different sequences I needed by parsing the global alignment result. But I think if diffseq can be implemented to use both local and global alignment to give the all different sequences directly, that will make it do the job as its name. Just a suggestion. Chunlei Stefanie Lager wrote: >diffseq use a local wordmatch alignment algorithm, it finds gaps but >at the ends you can't match against NOTHING. Try using a global >alignment algorithm instead (e.g. needle or stretcher). But maybe it >could be an option in diffseq to use either use a local or global >alignment algorithm? > >Stefanie > > > >>Hi, Group, >>I have one copy of EMBOSS (ver2.5.1) installed locally under >>cygwin/win2k. I expected "diffseq" can do the job as its name. >>However, I found it can not identify the different sequence at the >>both ends of input sequences. Only the different seq. inside can >>be indentified. Why? Is it the design purpose? How can I get all >>different sequences I need? >> >>Thank you. >> >>Chunlei >> >> >> >> > >_________________________________________________________________ > http://fastmail.ca/ - Fast Secure Web Email for Canadians > From ableasby at hgmp.mrc.ac.uk Tue Jan 21 13:30:16 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 21 Jan 2003 18:30:16 GMT Subject: EMBOSS 2.6.0 released Message-ID: <200301211830.SAA25776@bromine.hgmp.mrc.ac.uk> EMBOSS-2.6.0 is now available for download from the homepage: http://www.uk.embnet.org/Software/EMBOSS or via ftp: ftp://ftp.uk.embnet.org/pub/EMBOSS/ The ChangeLog shows useful information. Highlights include the addition of new programs (e.g. SIXPACK and PESTFIND) and the first release candidate 1.0 version of Jemboss (see below). Protein structure programs have been bundled together into the new embassy package DOMAINATRIX so there is a more clear distinction between sequence and structure analysis software. It is still to be regarded as part of the main EMBOSS package and, of course, maintains its GPL status. All embassy packages have been re-bundled for this new release. Jemboss-1.0-rc1 =============== Features include: -first release of Jemboss that uses the new Apache Axis (1.0) for the SOAP protocol. The client and server now use Axis calls to communicate and for data transfer. - speed-up of the interface launching process; wossname.jar (containing the output of wossname) is wrapped with the client and the server is just queried for the database names and available scoring matrices on startup. This means that the interface can almost immediately spring into life and EMBOSS applications selected while the SOAP connection is made with the server. - the installation script has been improved to simplify installation of a server. - the ability to set up both client-server and standalone modes with the installation script. - saving of the local working directory between sessions. Alan From squiresb at macrogenics.com Tue Jan 21 16:11:44 2003 From: squiresb at macrogenics.com (Burke Squires) Date: Tue, 21 Jan 2003 15:11:44 -0600 Subject: CAI tables origin In-Reply-To: Message-ID: Hello, I am interested in learning what genes went into the CAI table, "ehum.cut", that are considered highly expressed. Does anybody know where I could download this list with sequence information? Sincerely, Burke Squires -- Burke Squires Bioinformatics MacroGenics, Inc. 2600 Stemmons Freeway, Suite 210 Dallas, TX 75235 USA Work: 214-634-3000 X224 Fax: 214-634-3002 ---------------------------------------------------------------------------- This e-mail and any attachments may be confidential or legally privileged. If you received this message in error or are not the intended recipient, you should destroy the e-mail message and any attachments or copies, and you are prohibited from retaining, distributing, disclosing or using any information contained herein. Please inform us of the erroneous delivery by return e-mail. Thank you for your cooperation. From fernan at iib.unsam.edu.ar Wed Jan 22 12:13:58 2003 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Wed, 22 Jan 2003 14:13:58 -0300 Subject: EMBASSY program suites Message-ID: <20030122171358.GF35269@iib.unsam.edu.ar> Hi, I've a question regarding EMBASSY apps. I'm now updating the EMBOSS FreeBSD port to the latest (2.6.0) version, and need to solve the problem of these associated apps. I see that some EMBASSY packages are very similar to EMBOSS apps. Seems like, as it is made clear on the web site, they share the same look and feel, but the author wishes to keep them separate from the rest of EMBOSS. Without knowing anything of the internals it would be OK to guess that they use or depend on some EMBOSS shared library or binaries? On the other hand, some packages like Phylip are usable on their own, and IIRC I've never needed to install EMBOSS to have a usable phylip installation. What is the purpose of having phylip as an associated app? How is this phylip different from the one provided by the author? I've noticed that the version of phylip in EMBASSY have lagged behind in the past, was this for some reason? My main interest with these questions, and regarding the FreeBSD EMBOSS port is to decide if I should direct users to the already existing port for phylip or if I need to create a new EMBOSS-specific phylip port (this could be needed if the phylip release used in EMBASSY needs to be different for some reason). The same happens with respect to the other packages, although currently there is no independent EMNU, TOPO or MSE ports in FreeBSD. Also, I guess (without too much knowledge) that perhaps these do integrate in some more tighter way with EMBOSS and perhaps (please enlighten me) cannot be installed independently. Thanks in advance for suggestions, corrections, clarifications, etc. Fernan -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan From fernan at iib.unsam.edu.ar Wed Jan 22 14:17:43 2003 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Wed, 22 Jan 2003 16:17:43 -0300 Subject: Antwort: EMBASSY program suites In-Reply-To: References: Message-ID: <20030122191743.GJ35269@iib.unsam.edu.ar> +----[ David.Bauer at SCHERING.DE (22.Jan.2003 15:41): | | Hello Fernan, Hi again, | Example: sim4 Now that you mention sim4, the following web page does not mention anything about it: According to this page there are only 4 EMBASSY apps ... and EMNU is now 1.0.5 instead of 1.0.4 ... Should I follow what I see at the FTP site? If I'm getting it right there are now 8 EMBASSY apps. Also, do I need to download Jemboss separately (Jemboss-1.0-rc1.zip from the ftp site) I see that EMBOSS-2.6.0.tar.gz includes a jemboss subdir already. Thanks again, Fernan | +----] -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan From sebastian.bassi at ar.advantaseeds.com Wed Jan 22 18:12:03 2003 From: sebastian.bassi at ar.advantaseeds.com (Sebastian Bassi) Date: Thu, 23 Jan 2003 00:12:03 +0100 Subject: EMBASSY program suites Message-ID: Hi, > On the other hand, some packages like Phylip are usable on > their own, and IIRC I've never needed to install EMBOSS to > have a usable phylip installation. What is the purpose of > having phylip as an associated app? How is this phylip > different from the one provided by the author? AFAIK, the "original" phylip comes with a text based menu and is aimed for an interactive use. But the "embossed" pyhlip runs as a command line program without any user input requested (you have to give all option using command line). Appart from that, the "embossed" programs supports the same input file format as EMBOSS. That's what I think, I'm not really sure (I always used phylip as a stand alone program, without EMBOSS). Best regards, Sebastian Bassi http://bioinfo.unq.edu.ar From starksb at ebi.ac.uk Tue Jan 28 08:26:06 2003 From: starksb at ebi.ac.uk (David Starks-Browning) Date: Tue, 28 Jan 2003 13:26:06 +0000 Subject: feature request -- "showdb" diagnostic Message-ID: <5493-Tue28Jan2003132606+0000-starksb@ebi.ac.uk> Greetings, Given that EMBOSS database configurations can come from 4 locations: - A file emboss.default in the share/EMBOSS subdirectory of your installation - A file .embossrc in the directory specified by the EMBOSSRC environment variable - A file .embossrc in the users home directory - A file .embossrc in the current directory I think it would be useful, for diagnostic purposes, for a command like "showdb" to report on what configuration files were read. For example, "showdb -debug" could contain this information. (Apologies if this has already been added, I only tried showdb in EMBOSS-2.5.1.) Thanks, David ------------------------------------------------------------------- David Starks-Browning | starksb at ebi.ac.uk EMBL Outstation -- | The European Bioinformatics Institute | Wellcome Trust Genome Campus | tel: +44 (1223) 494 616 Hinxton, Cambridge, CB10 1SD, UK | fax: +44 (1223) 494 468 ------------------------------------------------------------------- From pmr at ebi.ac.uk Tue Jan 28 09:15:53 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 28 Jan 2003 14:15:53 +0000 Subject: feature request -- "showdb" diagnostic References: <5493-Tue28Jan2003132606+0000-starksb@ebi.ac.uk> Message-ID: <3E369099.4060602@ebi.ac.uk> David Starks-Browning wrote: > I think it would be useful, for diagnostic purposes, for a command > like "showdb" to report on what configuration files were read. For > example, "showdb -debug" could contain this information. This fits nicely with improved diagnostic messages for problems in defining databases (etc.). I will add something to the database definition internals for the next release. regards, Peter Rice From haruna at sgi.com Tue Jan 28 13:28:45 2003 From: haruna at sgi.com (Haruna Cofer) Date: Tue, 28 Jan 2003 13:28:45 -0500 Subject: EMBOSS 2.6.0 for SGI/IRIX Message-ID: <3E36CBDD.377FBEFB@sgi.com> Hello there -- Just FYI, I have updated my porting notes for the latest 2.6.0 release of the EMBOSS, EMBASSY, and Jemboss programs on SGI IRIX systems: http://www.sgi.com/industries/sciences/chembio/resources/emboss/ Many thanks to those of you who have reviewed and sent corrections for my porting notes! Thanks again, and take care! -- Haruna :) -- Haruna N. Cofer Silicon Graphics Inc. ChemPharm Applications From mad at biol.unlp.edu.ar Wed Jan 29 06:45:48 2003 From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=) Date: Wed, 29 Jan 2003 08:45:48 -0300 Subject: tfextract problem Message-ID: <3E37BEEC.4020706@biol.unlp.edu.ar> Hi, we're having a problem with transfac, it generates empty files. Here is the output: > # tfextract > Extract data from TRANSFAC > Full pathname of transfac SITE.DAT: /home/dbs/flatfiles/transfac/site.dat > # ls -1s /usr/local/emboss/share/EMBOSS/data/tf* > 0 /usr/local/emboss/share/EMBOSS/data/tffungi > 0 /usr/local/emboss/share/EMBOSS/data/tfinsect > 0 /usr/local/emboss/share/EMBOSS/data/tfother > 0 /usr/local/emboss/share/EMBOSS/data/tfplant > 0 /usr/local/emboss/share/EMBOSS/data/tfvertebrate > # It does not give any error. Here's a sample of site.dat > VV TRANSFAC SITES TABLE, V.2.4 25-08-1995 > XX > // > AC R00001 > XX > ID HS$6-16_01 > XX > DT 20.06.90 (created); . ........ > SO 0811; B103 > ME gel shift competition > RN [1] > RA Suzuki-Yagawa Y., Kawakami K., Nagano K. > RT Housekeeping Na,K-ATPase alpha1 subunit gene promoter is composed > RT of multiple cis elements to which common and cell type-specific > RT factors bind > RL Mol. Cell. Biol. 12:4046-4055 (1992). > DR EMBL; X52560; HSNFIL6(37:74). > // We're using EMBOSS 2.4.1 Thanks for helping, martin -- Mart?n Sarachu mad at biol.unlp.edu.ar EMBNet Argentina http://www.ar.embnet.org From axel.klenk at morphochem.ch Wed Jan 29 11:34:04 2003 From: axel.klenk at morphochem.ch (axel klenk) Date: Wed, 29 Jan 2003 17:34:04 +0100 Subject: problem with dbiflat (?) Message-ID: <01C2C7BC.9F4714D0.axel.klenk@morphochem.ch> Hi all, I have a problem with dbiflat (I suppose) and the index created for SWISS-PROT 40.41 yesterday. Some sequence ids (9,401 to be precise) cannot be retrieved by any EMBOSS program as single sequences, but they are found when searching with wildcards (see examples below). This happens only with SWISS-PROT, there are no problems with TrEMBL, EMBL nor any other of our databases; and it happens with dbiflat indexes from EMBOSS 2.4.1 and 2.6.0. The package has been built using gcc 2.95.3 on Solaris 8. Is this a known problem and are there any solutions for it? I have attached some funny examples and a debug file that might help. Thanks in advance, - axel klenk ---------------------------------------- axel klenk morphochem AG wro-1055 schwarzwaldallee 215 4058 basel tel. ++41-61-6952104 fax ++41-61-6952122 axel.klenk at morphochem.ch http://www.morphochem.ch Details: dbiflat builds the index without any complaint: mbsun01:/data/bioinfo/emboss/swissprot/40.41> dbiflat Index a flat file database EMBL : EMBL SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew GB : Genbank, DDBJ REFSEQ : Refseq Entry format [SWISS]: Database directory [.]: /data/bioinfo/db/swissprot/latest Wildcard database filename [*.dat]: sprot.dat Database name: sw Release number [0.0]: 40.41 Index date [00/00/00]: 01/29/03 mbsun01:/data/bioinfo/emboss/swissprot/40.41> ll total 10018 -rw-r--r-- 1 bioinfo bioinfo 591864 Jan 29 16:36 acnum.hit -rw-r--r-- 1 bioinfo bioinfo 2068590 Jan 29 16:36 acnum.trg -rw-r--r-- 1 bioinfo bioinfo 346 Jan 29 16:36 division.lkp -rw-r--r-- 1 bioinfo bioinfo 2430600 Jan 29 16:36 entrynam.idx it finds: dyr*_ecoli and dyrf_ecoli but not dyr_ecoli nor dyra_ecoli nor dyra* and only some dyrb*s: mbsun01:/export/home/aklenk/tmp> infoseq sw:dyr\*_ecoli Displays some simple information about sequences # USA Name Accession Type Length Description sw-id:DYR1_ECOLI DYR1_ECOLI P00382 P 157 Dihydrofolate reductase type I (EC 1.5.1.3) (Trimethoprim resistance protein). sw-id:DYR5_ECOLI DYR5_ECOLI P11731 P 157 Dihydrofolate reductase type V (EC 1.5.1.3). sw-id:DYR7_ECOLI DYR7_ECOLI P27422 P 157 Dihydrofolate reductase type VII (EC 1.5.1.3). sw-id:DYR8_ECOLI DYR8_ECOLI Q57452 P 169 Dihydrofolate reductase type VIII (EC 1.5.1.3) (DHFR type IIIC). sw-id:DYR9_ECOLI DYR9_ECOLI Q59397 P 177 Dihydrofolate reductase type IX (EC 1.5.1.3). sw-id:DYRA_ECOLI DYRA_ECOLI Q04515 P 187 Dihydrofolate reductase type X (EC 1.5.1.3). sw-id:DYRC_ECOLI DYRC_ECOLI Q59408 P 165 Dihydrofolate reductase type XIII (EC 1.5.1.3). sw-id:DYRF_ECOLI DYRF_ECOLI P78218 P 157 Dihydrofolate reductase type XV (EC 1.5.1.3). sw-id:DYR_ECOLI DYR_ECOLI P00379 P 159 Dihydrofolate reductase (EC 1.5.1.3). mbsun01:/export/home/aklenk/tmp> infoseq sw:dyrf_ecoli Displays some simple information about sequences # USA Name Accession Type Length Description sw-id:DYRF_ECOLI DYRF_ECOLI P78218 P 157 Dihydrofolate reductase type XV (EC 1.5.1.3). mbsun01:/export/home/aklenk/tmp> infoseq sw:dyra_ecoli Displays some simple information about sequences Error: Database Entry 'dyra_ecoli' not found Error: Unable to read sequence 'sw:dyra_ecoli' Died: infoseq terminated: Bad value for option [sequence] and no prompt mbsun01:/export/home/aklenk/tmp> infoseq sw:dyr_ecoli Displays some simple information about sequences Error: Database Entry 'dyr_ecoli' not found Error: Unable to read sequence 'sw:dyr_ecoli' Died: infoseq terminated: Bad value for option [sequence] and no prompt mbsun01:/export/home/aklenk/tmp> infoseq sw:dyra\* Displays some simple information about sequences Error: Database Query 'dyra*' not found Error: Unable to read sequence 'sw:dyra*' Died: infoseq terminated: Bad value for option [sequence] and no prompt mbsun01:/export/home/aklenk/tmp> infoseq sw:dyrb\* Displays some simple information about sequences # USA Name Accession Type Length Description sw-id:DYRB_MOUSE DYRB_MOUSE Q9Z188 P 589 Dual-specificity tyrosine-phosphorylation regulated kinase 1B (EC 2.7.1.-). sw-id:DYRB_STAAM DYRB_STAAM P10167 P 158 Dihydrofolate reductase type I (EC 1.5.1.3). mbsun01:/export/home/aklenk/tmp> infoseq sw:dyr\* | grep -i dyrb Displays some simple information about sequences sw-id:DYRB_HUMAN DYRB_HUMAN Q9Y463 P 629 Dual-specificity tyrosine-phosphorylation regulated kinase 1B (EC 2.7.1.-) (Mirk protein kinase). sw-id:DYRB_MOUSE DYRB_MOUSE Q9Z188 P 589 Dual-specificity tyrosine-phosphorylation regulated kinase 1B (EC 2.7.1.-). sw-id:DYRB_STAAM DYRB_STAAM P10167 P 158 Dihydrofolate reductase type I (EC 1.5.1.3). -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/octet-stream Size: 17537 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20030129/2038efd0/attachment.obj From ableasby at hgmp.mrc.ac.uk Wed Jan 29 12:18:05 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 29 Jan 2003 17:18:05 GMT Subject: problem with dbiflat (?) Message-ID: <200301291718.RAA22693@hydrogen.hgmp.mrc.ac.uk> It may be your system sort is not set up to collate strictly. Try doing a setenv LC_COLLATE C and then reindexing. Alan From fernan at iib.unsam.edu.ar Fri Jan 31 11:43:21 2003 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Fri, 31 Jan 2003 13:43:21 -0300 Subject: running Jemboss after EMBOSS installation Message-ID: <20030131155904.GA39923@iib.unsam.edu.ar> Hi! I finally got EMBOSS-2.6.0 and all the EMBASSY packages ported to FreeBSD. I am about to submit the port to the FreeBSD ports system. However, I have some issues with Jemboss: Apparently all of the jemboss stuff gets installed in appropriate places. I see an ELF binary (jembossctl) and a shell script (runJemboss.csh) in PREFIX/bin; and a whole tree of various things at PREFIX/share/EMBOSS/jemboss i) is it everything ready to run Jemboss? I have both a native jdk (v1.3.1) and a linux-jdk (v.1.3.1) and with either of these I get the same error: [fernan at pi] /var/tmp/port_test/bin/runJemboss.csh [fernan at pi] Exception in thread "main" java.lang.NoClassDefFoundError: org/emboss/jemboss/Jemboss Or perhaps I should tweak some files manually? The runJemboss.csh file has all instances of PREFIX correctly replaced by /var/tmp/port_test (the PREFIX I used to test everything). ii) I noticed that the runJemboss.csh script that gets installed into PREFIX/bin differs from the one in PREFIX/share/EMBOSS/jemboss, and I also saw some instructions at the web site, regarding both standalone and client-server modes ... it is not clear to me which one I'm going to get with a plain EMBOSS installation. Thanks in advance for any tip or suggestion, Fernan -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan From tcarver at hgmp.mrc.ac.uk Fri Jan 31 12:47:41 2003 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Fri, 31 Jan 2003 17:47:41 +0000 (GMT) Subject: running Jemboss after EMBOSS installation In-Reply-To: <20030131155904.GA39923@iib.unsam.edu.ar> Message-ID: Hi Fernan There is an install script provided in EMBOSS-2.6.0/jemboss/utils, that installs EMBOSS and Jemboss (along with Tomcat and Axis if you are doing a server installation). It compiles EMBOSS with the --with-java and --with-javaos flags and --with-thread=$PLATFORM. The script compiles Jemboss and adds the Axis library to Tomcat. It will also deploy the Axis (SOAP) methods that Jemboss can access. The script is described further at: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Jemboss/install/setup.html If you do a plain EMBOSS installation Jemboss is not installed at all. Hope this helps. Best regards Tim Carver > i) is it everything ready to run Jemboss? I have both a > native jdk (v1.3.1) and a linux-jdk (v.1.3.1) and with > either of these I get the same error: > [fernan at pi] /var/tmp/port_test/bin/runJemboss.csh > [fernan at pi] Exception in thread "main" java.lang.NoClassDefFoundError: org/emboss/jemboss/Jemboss > Or perhaps I should tweak some files manually? > The runJemboss.csh file has all instances of PREFIX > correctly replaced by /var/tmp/port_test (the PREFIX I used > to test everything). > > ii) I noticed that the runJemboss.csh script that gets > installed into PREFIX/bin differs from the one in > PREFIX/share/EMBOSS/jemboss, and I also saw some > instructions at the web site, regarding both standalone and > client-server modes ... it is not clear to me which one I'm > going to get with a plain EMBOSS installation. > > Thanks in advance for any tip or suggestion, > > Fernan > > -- > F e r n a n A g u e r o > http://genoma.unsam.edu.ar/~fernan > From fernan at iib.unsam.edu.ar Fri Jan 31 13:50:57 2003 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Fri, 31 Jan 2003 15:50:57 -0300 Subject: running Jemboss after EMBOSS installation In-Reply-To: References: <20030131155904.GA39923@iib.unsam.edu.ar> Message-ID: <20030131185057.GB95797@iib.unsam.edu.ar> +----[ Dr T. Carver (31.Jan.2003 14:55): | | Hi Fernan Hi Tim, | There is an install script provided in EMBOSS-2.6.0/jemboss/utils, that | installs EMBOSS and Jemboss (along with Tomcat and Axis if you are doing | a server installation). It compiles EMBOSS with the --with-java and | --with-javaos flags and --with-thread=$PLATFORM. The script compiles | Jemboss and adds the Axis library to Tomcat. It will also deploy the Axis | (SOAP) methods that Jemboss can access. I see. Actually I already got there and was trying to make sense of what the install script did. In the case of a standalone server, and as far as I can see, the script just invokes configure, make and make install, passing some extra arguments, and then goes into running a few commands (java stuff that I don't understand), and finally producing a jemboss.properties file. Now, what if I -- without using the script at all -- try to build EMBOSS using the same flags, will this produce a working Jemboss? I ask this because I want to include Jemboss as an option in the FreeBSD port. My idea regarding this is to include functionality from install-jemboss.sh into the Makefile, and let the users say: make WITH_JEMBOSS=yes and have everything dealt with automagically. This is because many of the other things your script does (checking for java versions, locations, etc.) are already dealt with by FreeBSD's included Makefiles (in this case bsd.java.mk). Thus I need only include a few lines from your script into the FreeBSD Makefile. I haven't tested it yet but my Makefile would look like the following (right now I'm only assuming a standalone Jemboss): .if defined(WITH_JEMBOSS) USE_JAVA= 1.3+ CONFIGURE_ARGS+= --with-java=${JAVA_HOME}/include \ --with-javaos=${JAVA_HOME}/include/${JAVA_OS:L} CONFIGURE_ENV+= PATH=${PATH}:${JAVA_HOME}/bin MAKE_ENV+= PATH=${PATH}:${JAVA_HOME}/bin .endif Now JAVA_HOME and JAVA_OS (freebsd) are defined in bsd.java.mk, and this in turn is included because I defined USE_JAVA. CONFIGURE_ENV and MAKE_ENV are variables that are passed to configure and make when they're invoked. Now, in my post-install target I have (taken from your script): .if defined(WITH_JEMBOSS) JEMBOSS= ${PREFIX}/share/EMBOSS/jemboss @ cd ${JEMBOSS} && \ ${PREFIX}/bin/wossname -colon -gui -outf wossname.out -auto @ ${JAVA_HOME}/bin/jar cvf ${JEMBOSS}/resources/wossname.jar wossname.out @ ${JAVA_HOME}/bin/javac -classpath ${JEMBOSS} ${JEMBOSS}/org/emboss/jemboss/server/JembossServer.java @ ${JAVA_HOME}/bin/javac -classpath ${JEMBOSS} ${JEMBOSS}/org/emboss/jemboss/server/JembossFileServer.java @ ${SED} -e 's|^#java org|java org|' -e 's|^java org.emboss.jemboss.Jemboss &|#java org.emboss.jemboss.Jemboss &|' \ -e 's|^#setenv EMBOSS_INSTALL.*|setenv EMBOSS_INSTALL $EMBOSS_INSTALL/lib|' \ -e 's|^#setenv LD_LIBRARY_PATH|setenv LD_LIBRARY_PATH|' \ ${JEMBOSS}/runJemboss.csh .endif I have yet to include stuff to generate the jemboss.properties file, but you get the idea. I'm going to try this and report back, but please share your opinions. Is there anything I missed? I know that this is not the best solution, since everytime you modify anything to your install script, I need to update the FreeBSD port. Perhaps this could be added to the main EMBOSS Makefile, now that Jemboss is at 1.0 and is _the_ official GUI? | If you do a plain EMBOSS installation Jemboss is not installed at all. What I see is that a plain EMBOSS installation does not produce a working Jemboss, but it nonetheless installs a PREFIX/share/EMBOSS/jemboss tree, and some files in PREFIX/bin. Perhaps this can be avoided in the case of plain EMBOSS installations? | Hope this helps. Indeed it is helping. Best regards, Fernan | +----] -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan From cbonnard at isrec-sg1.unil.ch Tue Jan 7 08:10:17 2003 From: cbonnard at isrec-sg1.unil.ch (Claude Bonnard) Date: Tue, 7 Jan 2003 09:10:17 +0100 Subject: systematic error message Message-ID: <10301070910.ZM27222@isrec-sg1> Hello, I have a message which shows up with every emboss program and I do not find where it is coming from. does someone have a clue? of more fenerally a method for such problems? the "-debug" swithc does not show any indication of the problem in the .dbg file. the current emboss.default looks ok (?) the message is : Error: Bad database attribute '' after that, the program runs as expected... Thanks for your help regards Claude -- Claude Bonnard Ph.D. ISREC (Swiss Institute for Experimental Cancer Research) Bioinformatics Group Ch des Boveresses 155 CH-1066 Epalinges Switzerland phone: [41-21]-692-5891 fax: [41-21]-652-6933 From pmr at ebi.ac.uk Tue Jan 7 09:40:16 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 07 Jan 2003 09:40:16 +0000 Subject: systematic error message References: <10301070910.ZM27222@isrec-sg1> Message-ID: <3E1AA080.E174CB88@ebi.ac.uk> Hi Claude, > Error: Bad database attribute '' > > after that, the program runs as expected... Somewhere in emboss.defaults (or .embossrc) you have a bad database definition. Most probably in the last change you made there. I will look into adding the database name to the error message to help find it in fiture releases. Also, maybe this should be a really fatal error... regards, Peter (now at EBI) From asen.nenov at metalife.de Thu Jan 9 07:40:48 2003 From: asen.nenov at metalife.de (Asen Nenov) Date: Thu, 9 Jan 2003 09:40:48 +0200 Subject: Sixpack missing Message-ID: <003e01c2b7b2$75338e90$3801a8c0@metalife.bg> Hello, I was trying to run Sixpackon my server after downloading EMBOSS 2.5.1. Unfortunately it does'n happened to be in the distribution. Could anyone have an explanation for this problem? [or it's just me ;-)] Any help appreciated. Regards Asen Nenov METALIFE AG - Sofia, Bulgaria asen.nenov at metalife.de www.metalife.de ++359 2 950 1802 From stefanielager at fastmail.ca Thu Jan 9 08:14:57 2003 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Thu, 9 Jan 2003 03:14:57 -0500 (EST) Subject: Sixpack missing Message-ID: <3E1D2F81.0000A1.96511@ns.interchange.ca> Sixpack PROBABLY belong to the new programs (Written (November 2002) - Thomas Laurent) which is due in the NEXT release. There are some other programs with the same status , like sirna. Stefanie > Hello, > > I was trying to run Sixpackon my server after downloading EMBOSS > 2.5.1. Unfortunately it does'n happened to be in the distribution. > Could anyone have an explanation for this problem? [or it's just > me ;-)] Any help appreciated. > > Regards > Asen Nenov > > METALIFE AG - Sofia, Bulgaria > asen.nenov at metalife.de > www.metalife.de > ++359 2 950 1802 _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From ruediger at sanbi.ac.za Fri Jan 10 10:11:47 2003 From: ruediger at sanbi.ac.za (Ruediger Braeuning) Date: Fri, 10 Jan 2003 12:11:47 +0200 (SAST) Subject: Schedule for new EMBOSS release Message-ID: <20030110121048.T6479-100000@fling.sanbi.ac.za> Hi everybody, I was wondering if a new release of EMBOSS is scheduled for the next days? Thanks Ruediger ------------------------------------------------------------------------- Ruediger Braeuning / South African National Bioinformatics Institute (=) University of the Western Cape Ph. +27 21 959 3645 / Private Bag X17 Fax +27 21 959 2512 (=) Bellville, 7535 www.sanbi.ac.za / South Africa From ableasby at hgmp.mrc.ac.uk Fri Jan 10 10:18:19 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 10 Jan 2003 10:18:19 GMT Subject: Schedule for new EMBOSS release Message-ID: <200301101018.KAA21210@bromine.hgmp.mrc.ac.uk> There will be a release soon. As has been pointed out on the group there have been a few new programs added. Alan From areagp61 at yahoo.it Fri Jan 10 13:30:37 2003 From: areagp61 at yahoo.it (Graziano P.) Date: Fri, 10 Jan 2003 14:30:37 +0100 Subject: seqretsplit Message-ID: <000c01c2b8ac$810e9f20$68b6ccc1@biologia.uniba.it> Hi all, I have a single file containing 164 sequences in embl format retrieved by SRS. I want to split all the entries in distinct files. I have tried to use "seqretsplit", but it do not report FT lines. For example: My entry retrieved by means of SRS is: ID AY045754_4; parent: AY045754AC AY045754; FT rRNA 610. .772 FT /product="5.8S ribosomal RNA" SQ Sequence 163 BP; TATATTCTAG CCTTATCGGT GGATCACTCG GCTCGTGGAT CGATGAAGAA CGCAGCCAAC 60 TGCGATAATT AGTGTGAACT GCAGAAACCT TGAACACTGA ACTTTCGAAT GCACATTGCG 120 CCATTGGAGT TATATCCATT GCACGCCTGG TTCAGGGTCG TAA 163 // but seqretsplit convert it in: ID AY045754_4 standard; DNA; UNC; 163 BP. SQ Sequence 163 BP; 43 A; 37 C; 39 G; 44 T; 0 other; TATATTCTAG CCTTATCGGT GGATCACTCG GCTCGTGGAT CGATGAAGAA CGCAGCCAAC 6 TGCGATAATT AGTGTGAACT GCAGAAACCT TGAACACTGA ACTTTCGAAT GCACATTGCG 12 CCATTGGAGT TATATCCATT GCACGCCTGG TTCAGGGTCG TAA 16 // Anyone knows an application or a script that allows me to split sequences (embl format) in different files without losing FT lines? Best regards Graziano -------------- next part -------------- An HTML attachment was scrubbed... URL: From pmr at ebi.ac.uk Fri Jan 10 14:36:53 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 10 Jan 2003 14:36:53 +0000 Subject: seqretsplit References: <000c01c2b8ac$810e9f20$68b6ccc1@biologia.uniba.it> Message-ID: <3E1EDA85.4080106@ebi.ac.uk> Ciao Graziono, > I have a single file containing 164 sequences in embl format > retrieved by SRS. I want to split all the entries in distinct files. I > have tried to use "seqretsplit", but it do not report FT lines. For example: > My entry retrieved by means of SRS is: > > ID AY045754_4; parent: AY045754AC AY045754; > FT rRNA 610. .772 > FT /product="5.8S ribosomal RNA" This must be a GCG format database, indexed in SRS ... you have gaps in the ".." format. Ideally SRS would fix that ... but EMBOSS could cope with some small changes. Anyway, an SRS fix is non-trivial because it is reporting exactly the text that GCG stores. > Anyone knows an application or a script that allows me to split > sequences (embl format) in different files without losing FT lines? Simplest in your case would be a script that changes ". ." to ".." before passing the data to EMBOSS. Meanwhile, I will take a look at fixing this for a future release. regards, Peter From kim at inb.uni-luebeck.de Tue Jan 14 16:07:19 2003 From: kim at inb.uni-luebeck.de (Jan T. Kim) Date: Tue, 14 Jan 2003 17:07:19 +0100 Subject: Nucleotide profiles with prophecy and profit? Message-ID: <20030114170719.C21341@pc10.inb.mu-luebeck.de> Dear EMBOSSers, we have recently attempted to use the programs prophecy and profit with nucleotide sequences, but we could not figure out how to do this. It appears that the prophecy program unconditionally assumes amino acid sequences -- even converting the FASTA formatted file to msf format and verifying that it says "Type: N" in that, prophecy insists on outputting a x 20 matrix instead of a x 4 one. It was also not possible to convince profit to accept a hand-written x 4 matrix. Could anyone point out to me how to proceed for search nucleotide sequences with a profile matrix? I have noticed the tfscan program, but it seems that employing this would require to construct some kind of mock-up TRANSFAC around my matrix just so I can scan sequences with that. Probably, I have overlooked the obvious and now started to think of twisted ways to do such a scan...? Thanks in advance for your help. Greetinx, Jan -- +- Jan T. Kim -------------------------------------------------------+ | *NEW* email: kim at inb.uni-luebeck.de | | *NEW* WWW: http://www.inb.uni-luebeck.de/staff/kim.html | *-----=< hierarchical systems are for files, not for humans >=-----* From p.ernst at dkfz-heidelberg.de Tue Jan 14 17:15:29 2003 From: p.ernst at dkfz-heidelberg.de (Peter Ernst) Date: Tue, 14 Jan 2003 18:15:29 +0100 (MET) Subject: Perl Module Bio-Emboss-0.1 released Message-ID: Hello, this is an announcement of the first test release of Bio::Emboss perl module version 0.1 =================================== This module interfaces to the libraries of the EMBOSS package. With this module you can access EMBOSS databases and use EMBOSS functions to manipulate data. You can write perl programs that look like any other EMBOSS program (command-line, web interface). SYNOPSIS use Bio::Emboss qw(:all); embInitPerl("seqret", \@ARGV); $seqall = ajAcdGetSeqall("sequence"); $seqout = ajAcdGetSeqoutall("outseq"); $firstonly = ajAcdGetBool ("firstonly"); while ($seqall->ajSeqallNext($seq)) { $seqout->ajSeqAllWrite ($seq); last if $firstonly; } DOWNLOAD ftp://genome.dkfz-heidelberg.de/pub/emboss/perl/ and CPAN (soon) REQUIREMENTS EMBOSS-2.5.1 (including sources) (I don't know if it will work with earlier versions.) STATUS There are interfaces to most (but not all) functions in libajax. There are only a few interfaces to functions in libnucleus. Most functions have *not* been tested yet (Emboss is big !), however a few test scripts are provided. AUTHOR Peter Ernst, -- ======================================================================= Peter Ernst Department of Molecular Biophysics - B020 Deutsches Krebsforschungszentrum (German Cancer Research Center) DKFZ Im Neuenheimer Feld 580 / Technologiepark 3 69120 Heidelberg, Germany phone: +49-6221-42-2330 http://genome.dkfz-heidelberg.de/ fax: +49-6221-42-2333 ======================================================================= From kellert at ohsu.edu Tue Jan 14 23:31:35 2003 From: kellert at ohsu.edu (Thomas Keller) Date: Tue, 14 Jan 2003 15:31:35 -0800 Subject: EMBOSS: abiview Message-ID: <5217F7D9-2818-11D7-8AB5-0003930405E2@ohsu.edu> Greetings, I'm a new EMBOSS user, so please be gentle. I'm using my local installation on a Mac running OS 10.2.1. "abiview": four color plot is generated, but -window option allows more bases, but how does one view for example bases 200-250? My home directory .embossrc file looks like this: # EMBOSS configuration file for kellert set emboss_acdroot /usr/local/biotools/share/EMBOSS/acd set emboss_database_dir /usr/local/biotools/data/dbs I source a file containing the following env variables when I launch a terminal or xterm window: set path=(/usr/local/biotools/bin $path) setenv MANPATH ${MANPATH}:/usr/local/biotools/man setenv WISECONFIGDIR /usr/local/biotools/wisecfg/ setenv EMBOSS_ACDROOT /usr/local/biotools/share/EMBOSS/acd setenv EMBOSS_DATA /usr/local/biotools/share/EMBOSS/data setenv PLPLOT_LIB /usr/local/biotools/share/EMBOSS Thanks, Tom K. Thomas J. Keller, Ph.D. Oregon Health & Science University MMI Research Core Facility 3181 SW Sam Jackson Park Rd. Portland, OR, USA, 97239 http://www.ohsu.edu/core -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1109 bytes Desc: not available URL: From newgene at bigfoot.com Wed Jan 15 02:29:11 2003 From: newgene at bigfoot.com (clwu) Date: Tue, 14 Jan 2003 20:29:11 -0600 Subject: Q on "diffseq" Message-ID: <3E24C777.8030808@bigfoot.com> Hi, Group, I have one copy of EMBOSS (ver2.5.1) installed locally under cygwin/win2k. I expected "diffseq" can do the job as its name. However, I found it can not identify the different sequence at the both ends of input sequences. Only the different seq. inside can be indentified. Why? Is it the design purpose? How can I get all different sequences I need? Thank you. Chunlei From grsvc at mucc.mahidol.ac.th Wed Jan 15 03:57:40 2003 From: grsvc at mucc.mahidol.ac.th (Suksiri Vichasri Grams) Date: Wed, 15 Jan 2003 10:57:40 +0700 Subject: EMBOSS: abiview In-Reply-To: <5217F7D9-2818-11D7-8AB5-0003930405E2@ohsu.edu> Message-ID: <7E095164-283D-11D7-9826-000393629C54@mucc.mahidol.ac.th> Hi, abiview has two options named -startbase and -endbase which can be used to limit the analysis to the entered values. Kindly, Rudi On Wednesday, Jan 15, 2003, at 06:31 Asia/Jakarta, Thomas Keller wrote: > Greetings, > I'm a new EMBOSS user, so please be gentle. > I'm using my local installation on a Mac running OS 10.2.1. > "abiview": four color plot is generated, but -window option allows > more bases, but how does one view for example bases 200-250? > My home directory .embossrc file looks like this: > # EMBOSS configuration file for kellert > set emboss_acdroot /usr/local/biotools/share/EMBOSS/acd > set emboss_database_dir /usr/local/biotools/data/dbs > > I source a file containing the following env variables when I launch a > terminal or xterm window: > set path=(/usr/local/biotools/bin $path) > setenv MANPATH ${MANPATH}:/usr/local/biotools/man > setenv WISECONFIGDIR /usr/local/biotools/wisecfg/ > setenv EMBOSS_ACDROOT /usr/local/biotools/share/EMBOSS/acd > setenv EMBOSS_DATA /usr/local/biotools/share/EMBOSS/data > setenv PLPLOT_LIB /usr/local/biotools/share/EMBOSS > > Thanks, > Tom K. > > Thomas J. Keller, Ph.D. > Oregon Health & Science University > MMI Research Core Facility > 3181 SW Sam Jackson Park Rd. > Portland, OR, USA, 97239 > > http://www.ohsu.edu/core > From stefanielager at fastmail.ca Wed Jan 15 07:44:58 2003 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Wed, 15 Jan 2003 02:44:58 -0500 (EST) Subject: Q on Message-ID: <3E25117A.000081.16653@ns.interchange.ca> diffseq use a local wordmatch alignment algorithm, it finds gaps but at the ends you can't match against NOTHING. Try using a global alignment algorithm instead (e.g. needle or stretcher). But maybe it could be an option in diffseq to use either use a local or global alignment algorithm? Stefanie > Hi, Group, > I have one copy of EMBOSS (ver2.5.1) installed locally under > cygwin/win2k. I expected "diffseq" can do the job as its name. > However, I found it can not identify the different sequence at the > both ends of input sequences. Only the different seq. inside can > be indentified. Why? Is it the design purpose? How can I get all > different sequences I need? > > Thank you. > > Chunlei > > _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From newgene at bigfoot.com Wed Jan 15 18:38:07 2003 From: newgene at bigfoot.com (clwu) Date: Wed, 15 Jan 2003 12:38:07 -0600 Subject: Q on References: <3E25117A.000081.16653@ns.interchange.ca> Message-ID: <3E25AA8F.4030304@bigfoot.com> Thank you, Stefanie. I can get the different sequences I needed by parsing the global alignment result. But I think if diffseq can be implemented to use both local and global alignment to give the all different sequences directly, that will make it do the job as its name. Just a suggestion. Chunlei Stefanie Lager wrote: >diffseq use a local wordmatch alignment algorithm, it finds gaps but >at the ends you can't match against NOTHING. Try using a global >alignment algorithm instead (e.g. needle or stretcher). But maybe it >could be an option in diffseq to use either use a local or global >alignment algorithm? > >Stefanie > > > >>Hi, Group, >>I have one copy of EMBOSS (ver2.5.1) installed locally under >>cygwin/win2k. I expected "diffseq" can do the job as its name. >>However, I found it can not identify the different sequence at the >>both ends of input sequences. Only the different seq. inside can >>be indentified. Why? Is it the design purpose? How can I get all >>different sequences I need? >> >>Thank you. >> >>Chunlei >> >> >> >> > >_________________________________________________________________ > http://fastmail.ca/ - Fast Secure Web Email for Canadians > From ableasby at hgmp.mrc.ac.uk Tue Jan 21 18:30:16 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 21 Jan 2003 18:30:16 GMT Subject: EMBOSS 2.6.0 released Message-ID: <200301211830.SAA25776@bromine.hgmp.mrc.ac.uk> EMBOSS-2.6.0 is now available for download from the homepage: http://www.uk.embnet.org/Software/EMBOSS or via ftp: ftp://ftp.uk.embnet.org/pub/EMBOSS/ The ChangeLog shows useful information. Highlights include the addition of new programs (e.g. SIXPACK and PESTFIND) and the first release candidate 1.0 version of Jemboss (see below). Protein structure programs have been bundled together into the new embassy package DOMAINATRIX so there is a more clear distinction between sequence and structure analysis software. It is still to be regarded as part of the main EMBOSS package and, of course, maintains its GPL status. All embassy packages have been re-bundled for this new release. Jemboss-1.0-rc1 =============== Features include: -first release of Jemboss that uses the new Apache Axis (1.0) for the SOAP protocol. The client and server now use Axis calls to communicate and for data transfer. - speed-up of the interface launching process; wossname.jar (containing the output of wossname) is wrapped with the client and the server is just queried for the database names and available scoring matrices on startup. This means that the interface can almost immediately spring into life and EMBOSS applications selected while the SOAP connection is made with the server. - the installation script has been improved to simplify installation of a server. - the ability to set up both client-server and standalone modes with the installation script. - saving of the local working directory between sessions. Alan From squiresb at macrogenics.com Tue Jan 21 21:11:44 2003 From: squiresb at macrogenics.com (Burke Squires) Date: Tue, 21 Jan 2003 15:11:44 -0600 Subject: CAI tables origin In-Reply-To: Message-ID: Hello, I am interested in learning what genes went into the CAI table, "ehum.cut", that are considered highly expressed. Does anybody know where I could download this list with sequence information? Sincerely, Burke Squires -- Burke Squires Bioinformatics MacroGenics, Inc. 2600 Stemmons Freeway, Suite 210 Dallas, TX 75235 USA Work: 214-634-3000 X224 Fax: 214-634-3002 ---------------------------------------------------------------------------- This e-mail and any attachments may be confidential or legally privileged. If you received this message in error or are not the intended recipient, you should destroy the e-mail message and any attachments or copies, and you are prohibited from retaining, distributing, disclosing or using any information contained herein. Please inform us of the erroneous delivery by return e-mail. Thank you for your cooperation. From fernan at iib.unsam.edu.ar Wed Jan 22 17:13:58 2003 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Wed, 22 Jan 2003 14:13:58 -0300 Subject: EMBASSY program suites Message-ID: <20030122171358.GF35269@iib.unsam.edu.ar> Hi, I've a question regarding EMBASSY apps. I'm now updating the EMBOSS FreeBSD port to the latest (2.6.0) version, and need to solve the problem of these associated apps. I see that some EMBASSY packages are very similar to EMBOSS apps. Seems like, as it is made clear on the web site, they share the same look and feel, but the author wishes to keep them separate from the rest of EMBOSS. Without knowing anything of the internals it would be OK to guess that they use or depend on some EMBOSS shared library or binaries? On the other hand, some packages like Phylip are usable on their own, and IIRC I've never needed to install EMBOSS to have a usable phylip installation. What is the purpose of having phylip as an associated app? How is this phylip different from the one provided by the author? I've noticed that the version of phylip in EMBASSY have lagged behind in the past, was this for some reason? My main interest with these questions, and regarding the FreeBSD EMBOSS port is to decide if I should direct users to the already existing port for phylip or if I need to create a new EMBOSS-specific phylip port (this could be needed if the phylip release used in EMBASSY needs to be different for some reason). The same happens with respect to the other packages, although currently there is no independent EMNU, TOPO or MSE ports in FreeBSD. Also, I guess (without too much knowledge) that perhaps these do integrate in some more tighter way with EMBOSS and perhaps (please enlighten me) cannot be installed independently. Thanks in advance for suggestions, corrections, clarifications, etc. Fernan -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan From fernan at iib.unsam.edu.ar Wed Jan 22 19:17:43 2003 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Wed, 22 Jan 2003 16:17:43 -0300 Subject: Antwort: EMBASSY program suites In-Reply-To: References: Message-ID: <20030122191743.GJ35269@iib.unsam.edu.ar> +----[ David.Bauer at SCHERING.DE (22.Jan.2003 15:41): | | Hello Fernan, Hi again, | Example: sim4 Now that you mention sim4, the following web page does not mention anything about it: According to this page there are only 4 EMBASSY apps ... and EMNU is now 1.0.5 instead of 1.0.4 ... Should I follow what I see at the FTP site? If I'm getting it right there are now 8 EMBASSY apps. Also, do I need to download Jemboss separately (Jemboss-1.0-rc1.zip from the ftp site) I see that EMBOSS-2.6.0.tar.gz includes a jemboss subdir already. Thanks again, Fernan | +----] -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan From sebastian.bassi at ar.advantaseeds.com Wed Jan 22 23:12:03 2003 From: sebastian.bassi at ar.advantaseeds.com (Sebastian Bassi) Date: Thu, 23 Jan 2003 00:12:03 +0100 Subject: EMBASSY program suites Message-ID: Hi, > On the other hand, some packages like Phylip are usable on > their own, and IIRC I've never needed to install EMBOSS to > have a usable phylip installation. What is the purpose of > having phylip as an associated app? How is this phylip > different from the one provided by the author? AFAIK, the "original" phylip comes with a text based menu and is aimed for an interactive use. But the "embossed" pyhlip runs as a command line program without any user input requested (you have to give all option using command line). Appart from that, the "embossed" programs supports the same input file format as EMBOSS. That's what I think, I'm not really sure (I always used phylip as a stand alone program, without EMBOSS). Best regards, Sebastian Bassi http://bioinfo.unq.edu.ar From starksb at ebi.ac.uk Tue Jan 28 13:26:06 2003 From: starksb at ebi.ac.uk (David Starks-Browning) Date: Tue, 28 Jan 2003 13:26:06 +0000 Subject: feature request -- "showdb" diagnostic Message-ID: <5493-Tue28Jan2003132606+0000-starksb@ebi.ac.uk> Greetings, Given that EMBOSS database configurations can come from 4 locations: - A file emboss.default in the share/EMBOSS subdirectory of your installation - A file .embossrc in the directory specified by the EMBOSSRC environment variable - A file .embossrc in the users home directory - A file .embossrc in the current directory I think it would be useful, for diagnostic purposes, for a command like "showdb" to report on what configuration files were read. For example, "showdb -debug" could contain this information. (Apologies if this has already been added, I only tried showdb in EMBOSS-2.5.1.) Thanks, David ------------------------------------------------------------------- David Starks-Browning | starksb at ebi.ac.uk EMBL Outstation -- | The European Bioinformatics Institute | Wellcome Trust Genome Campus | tel: +44 (1223) 494 616 Hinxton, Cambridge, CB10 1SD, UK | fax: +44 (1223) 494 468 ------------------------------------------------------------------- From pmr at ebi.ac.uk Tue Jan 28 14:15:53 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 28 Jan 2003 14:15:53 +0000 Subject: feature request -- "showdb" diagnostic References: <5493-Tue28Jan2003132606+0000-starksb@ebi.ac.uk> Message-ID: <3E369099.4060602@ebi.ac.uk> David Starks-Browning wrote: > I think it would be useful, for diagnostic purposes, for a command > like "showdb" to report on what configuration files were read. For > example, "showdb -debug" could contain this information. This fits nicely with improved diagnostic messages for problems in defining databases (etc.). I will add something to the database definition internals for the next release. regards, Peter Rice From haruna at sgi.com Tue Jan 28 18:28:45 2003 From: haruna at sgi.com (Haruna Cofer) Date: Tue, 28 Jan 2003 13:28:45 -0500 Subject: EMBOSS 2.6.0 for SGI/IRIX Message-ID: <3E36CBDD.377FBEFB@sgi.com> Hello there -- Just FYI, I have updated my porting notes for the latest 2.6.0 release of the EMBOSS, EMBASSY, and Jemboss programs on SGI IRIX systems: http://www.sgi.com/industries/sciences/chembio/resources/emboss/ Many thanks to those of you who have reviewed and sent corrections for my porting notes! Thanks again, and take care! -- Haruna :) -- Haruna N. Cofer Silicon Graphics Inc. ChemPharm Applications From mad at biol.unlp.edu.ar Wed Jan 29 11:45:48 2003 From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=) Date: Wed, 29 Jan 2003 08:45:48 -0300 Subject: tfextract problem Message-ID: <3E37BEEC.4020706@biol.unlp.edu.ar> Hi, we're having a problem with transfac, it generates empty files. Here is the output: > # tfextract > Extract data from TRANSFAC > Full pathname of transfac SITE.DAT: /home/dbs/flatfiles/transfac/site.dat > # ls -1s /usr/local/emboss/share/EMBOSS/data/tf* > 0 /usr/local/emboss/share/EMBOSS/data/tffungi > 0 /usr/local/emboss/share/EMBOSS/data/tfinsect > 0 /usr/local/emboss/share/EMBOSS/data/tfother > 0 /usr/local/emboss/share/EMBOSS/data/tfplant > 0 /usr/local/emboss/share/EMBOSS/data/tfvertebrate > # It does not give any error. Here's a sample of site.dat > VV TRANSFAC SITES TABLE, V.2.4 25-08-1995 > XX > // > AC R00001 > XX > ID HS$6-16_01 > XX > DT 20.06.90 (created); . ........ > SO 0811; B103 > ME gel shift competition > RN [1] > RA Suzuki-Yagawa Y., Kawakami K., Nagano K. > RT Housekeeping Na,K-ATPase alpha1 subunit gene promoter is composed > RT of multiple cis elements to which common and cell type-specific > RT factors bind > RL Mol. Cell. Biol. 12:4046-4055 (1992). > DR EMBL; X52560; HSNFIL6(37:74). > // We're using EMBOSS 2.4.1 Thanks for helping, martin -- Mart?n Sarachu mad at biol.unlp.edu.ar EMBNet Argentina http://www.ar.embnet.org From axel.klenk at morphochem.ch Wed Jan 29 16:34:04 2003 From: axel.klenk at morphochem.ch (axel klenk) Date: Wed, 29 Jan 2003 17:34:04 +0100 Subject: problem with dbiflat (?) Message-ID: <01C2C7BC.9F4714D0.axel.klenk@morphochem.ch> Hi all, I have a problem with dbiflat (I suppose) and the index created for SWISS-PROT 40.41 yesterday. Some sequence ids (9,401 to be precise) cannot be retrieved by any EMBOSS program as single sequences, but they are found when searching with wildcards (see examples below). This happens only with SWISS-PROT, there are no problems with TrEMBL, EMBL nor any other of our databases; and it happens with dbiflat indexes from EMBOSS 2.4.1 and 2.6.0. The package has been built using gcc 2.95.3 on Solaris 8. Is this a known problem and are there any solutions for it? I have attached some funny examples and a debug file that might help. Thanks in advance, - axel klenk ---------------------------------------- axel klenk morphochem AG wro-1055 schwarzwaldallee 215 4058 basel tel. ++41-61-6952104 fax ++41-61-6952122 axel.klenk at morphochem.ch http://www.morphochem.ch Details: dbiflat builds the index without any complaint: mbsun01:/data/bioinfo/emboss/swissprot/40.41> dbiflat Index a flat file database EMBL : EMBL SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew GB : Genbank, DDBJ REFSEQ : Refseq Entry format [SWISS]: Database directory [.]: /data/bioinfo/db/swissprot/latest Wildcard database filename [*.dat]: sprot.dat Database name: sw Release number [0.0]: 40.41 Index date [00/00/00]: 01/29/03 mbsun01:/data/bioinfo/emboss/swissprot/40.41> ll total 10018 -rw-r--r-- 1 bioinfo bioinfo 591864 Jan 29 16:36 acnum.hit -rw-r--r-- 1 bioinfo bioinfo 2068590 Jan 29 16:36 acnum.trg -rw-r--r-- 1 bioinfo bioinfo 346 Jan 29 16:36 division.lkp -rw-r--r-- 1 bioinfo bioinfo 2430600 Jan 29 16:36 entrynam.idx it finds: dyr*_ecoli and dyrf_ecoli but not dyr_ecoli nor dyra_ecoli nor dyra* and only some dyrb*s: mbsun01:/export/home/aklenk/tmp> infoseq sw:dyr\*_ecoli Displays some simple information about sequences # USA Name Accession Type Length Description sw-id:DYR1_ECOLI DYR1_ECOLI P00382 P 157 Dihydrofolate reductase type I (EC 1.5.1.3) (Trimethoprim resistance protein). sw-id:DYR5_ECOLI DYR5_ECOLI P11731 P 157 Dihydrofolate reductase type V (EC 1.5.1.3). sw-id:DYR7_ECOLI DYR7_ECOLI P27422 P 157 Dihydrofolate reductase type VII (EC 1.5.1.3). sw-id:DYR8_ECOLI DYR8_ECOLI Q57452 P 169 Dihydrofolate reductase type VIII (EC 1.5.1.3) (DHFR type IIIC). sw-id:DYR9_ECOLI DYR9_ECOLI Q59397 P 177 Dihydrofolate reductase type IX (EC 1.5.1.3). sw-id:DYRA_ECOLI DYRA_ECOLI Q04515 P 187 Dihydrofolate reductase type X (EC 1.5.1.3). sw-id:DYRC_ECOLI DYRC_ECOLI Q59408 P 165 Dihydrofolate reductase type XIII (EC 1.5.1.3). sw-id:DYRF_ECOLI DYRF_ECOLI P78218 P 157 Dihydrofolate reductase type XV (EC 1.5.1.3). sw-id:DYR_ECOLI DYR_ECOLI P00379 P 159 Dihydrofolate reductase (EC 1.5.1.3). mbsun01:/export/home/aklenk/tmp> infoseq sw:dyrf_ecoli Displays some simple information about sequences # USA Name Accession Type Length Description sw-id:DYRF_ECOLI DYRF_ECOLI P78218 P 157 Dihydrofolate reductase type XV (EC 1.5.1.3). mbsun01:/export/home/aklenk/tmp> infoseq sw:dyra_ecoli Displays some simple information about sequences Error: Database Entry 'dyra_ecoli' not found Error: Unable to read sequence 'sw:dyra_ecoli' Died: infoseq terminated: Bad value for option [sequence] and no prompt mbsun01:/export/home/aklenk/tmp> infoseq sw:dyr_ecoli Displays some simple information about sequences Error: Database Entry 'dyr_ecoli' not found Error: Unable to read sequence 'sw:dyr_ecoli' Died: infoseq terminated: Bad value for option [sequence] and no prompt mbsun01:/export/home/aklenk/tmp> infoseq sw:dyra\* Displays some simple information about sequences Error: Database Query 'dyra*' not found Error: Unable to read sequence 'sw:dyra*' Died: infoseq terminated: Bad value for option [sequence] and no prompt mbsun01:/export/home/aklenk/tmp> infoseq sw:dyrb\* Displays some simple information about sequences # USA Name Accession Type Length Description sw-id:DYRB_MOUSE DYRB_MOUSE Q9Z188 P 589 Dual-specificity tyrosine-phosphorylation regulated kinase 1B (EC 2.7.1.-). sw-id:DYRB_STAAM DYRB_STAAM P10167 P 158 Dihydrofolate reductase type I (EC 1.5.1.3). mbsun01:/export/home/aklenk/tmp> infoseq sw:dyr\* | grep -i dyrb Displays some simple information about sequences sw-id:DYRB_HUMAN DYRB_HUMAN Q9Y463 P 629 Dual-specificity tyrosine-phosphorylation regulated kinase 1B (EC 2.7.1.-) (Mirk protein kinase). sw-id:DYRB_MOUSE DYRB_MOUSE Q9Z188 P 589 Dual-specificity tyrosine-phosphorylation regulated kinase 1B (EC 2.7.1.-). sw-id:DYRB_STAAM DYRB_STAAM P10167 P 158 Dihydrofolate reductase type I (EC 1.5.1.3). -------------- next part -------------- A non-text attachment was scrubbed... Name: infoseq.dbg Type: application/octet-stream Size: 17537 bytes Desc: not available URL: From ableasby at hgmp.mrc.ac.uk Wed Jan 29 17:18:05 2003 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Wed, 29 Jan 2003 17:18:05 GMT Subject: problem with dbiflat (?) Message-ID: <200301291718.RAA22693@hydrogen.hgmp.mrc.ac.uk> It may be your system sort is not set up to collate strictly. Try doing a setenv LC_COLLATE C and then reindexing. Alan From fernan at iib.unsam.edu.ar Fri Jan 31 16:43:21 2003 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Fri, 31 Jan 2003 13:43:21 -0300 Subject: running Jemboss after EMBOSS installation Message-ID: <20030131155904.GA39923@iib.unsam.edu.ar> Hi! I finally got EMBOSS-2.6.0 and all the EMBASSY packages ported to FreeBSD. I am about to submit the port to the FreeBSD ports system. However, I have some issues with Jemboss: Apparently all of the jemboss stuff gets installed in appropriate places. I see an ELF binary (jembossctl) and a shell script (runJemboss.csh) in PREFIX/bin; and a whole tree of various things at PREFIX/share/EMBOSS/jemboss i) is it everything ready to run Jemboss? I have both a native jdk (v1.3.1) and a linux-jdk (v.1.3.1) and with either of these I get the same error: [fernan at pi] /var/tmp/port_test/bin/runJemboss.csh [fernan at pi] Exception in thread "main" java.lang.NoClassDefFoundError: org/emboss/jemboss/Jemboss Or perhaps I should tweak some files manually? The runJemboss.csh file has all instances of PREFIX correctly replaced by /var/tmp/port_test (the PREFIX I used to test everything). ii) I noticed that the runJemboss.csh script that gets installed into PREFIX/bin differs from the one in PREFIX/share/EMBOSS/jemboss, and I also saw some instructions at the web site, regarding both standalone and client-server modes ... it is not clear to me which one I'm going to get with a plain EMBOSS installation. Thanks in advance for any tip or suggestion, Fernan -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan From tcarver at hgmp.mrc.ac.uk Fri Jan 31 17:47:41 2003 From: tcarver at hgmp.mrc.ac.uk (Dr T. Carver) Date: Fri, 31 Jan 2003 17:47:41 +0000 (GMT) Subject: running Jemboss after EMBOSS installation In-Reply-To: <20030131155904.GA39923@iib.unsam.edu.ar> Message-ID: Hi Fernan There is an install script provided in EMBOSS-2.6.0/jemboss/utils, that installs EMBOSS and Jemboss (along with Tomcat and Axis if you are doing a server installation). It compiles EMBOSS with the --with-java and --with-javaos flags and --with-thread=$PLATFORM. The script compiles Jemboss and adds the Axis library to Tomcat. It will also deploy the Axis (SOAP) methods that Jemboss can access. The script is described further at: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Jemboss/install/setup.html If you do a plain EMBOSS installation Jemboss is not installed at all. Hope this helps. Best regards Tim Carver > i) is it everything ready to run Jemboss? I have both a > native jdk (v1.3.1) and a linux-jdk (v.1.3.1) and with > either of these I get the same error: > [fernan at pi] /var/tmp/port_test/bin/runJemboss.csh > [fernan at pi] Exception in thread "main" java.lang.NoClassDefFoundError: org/emboss/jemboss/Jemboss > Or perhaps I should tweak some files manually? > The runJemboss.csh file has all instances of PREFIX > correctly replaced by /var/tmp/port_test (the PREFIX I used > to test everything). > > ii) I noticed that the runJemboss.csh script that gets > installed into PREFIX/bin differs from the one in > PREFIX/share/EMBOSS/jemboss, and I also saw some > instructions at the web site, regarding both standalone and > client-server modes ... it is not clear to me which one I'm > going to get with a plain EMBOSS installation. > > Thanks in advance for any tip or suggestion, > > Fernan > > -- > F e r n a n A g u e r o > http://genoma.unsam.edu.ar/~fernan > From fernan at iib.unsam.edu.ar Fri Jan 31 18:50:57 2003 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Fri, 31 Jan 2003 15:50:57 -0300 Subject: running Jemboss after EMBOSS installation In-Reply-To: References: <20030131155904.GA39923@iib.unsam.edu.ar> Message-ID: <20030131185057.GB95797@iib.unsam.edu.ar> +----[ Dr T. Carver (31.Jan.2003 14:55): | | Hi Fernan Hi Tim, | There is an install script provided in EMBOSS-2.6.0/jemboss/utils, that | installs EMBOSS and Jemboss (along with Tomcat and Axis if you are doing | a server installation). It compiles EMBOSS with the --with-java and | --with-javaos flags and --with-thread=$PLATFORM. The script compiles | Jemboss and adds the Axis library to Tomcat. It will also deploy the Axis | (SOAP) methods that Jemboss can access. I see. Actually I already got there and was trying to make sense of what the install script did. In the case of a standalone server, and as far as I can see, the script just invokes configure, make and make install, passing some extra arguments, and then goes into running a few commands (java stuff that I don't understand), and finally producing a jemboss.properties file. Now, what if I -- without using the script at all -- try to build EMBOSS using the same flags, will this produce a working Jemboss? I ask this because I want to include Jemboss as an option in the FreeBSD port. My idea regarding this is to include functionality from install-jemboss.sh into the Makefile, and let the users say: make WITH_JEMBOSS=yes and have everything dealt with automagically. This is because many of the other things your script does (checking for java versions, locations, etc.) are already dealt with by FreeBSD's included Makefiles (in this case bsd.java.mk). Thus I need only include a few lines from your script into the FreeBSD Makefile. I haven't tested it yet but my Makefile would look like the following (right now I'm only assuming a standalone Jemboss): .if defined(WITH_JEMBOSS) USE_JAVA= 1.3+ CONFIGURE_ARGS+= --with-java=${JAVA_HOME}/include \ --with-javaos=${JAVA_HOME}/include/${JAVA_OS:L} CONFIGURE_ENV+= PATH=${PATH}:${JAVA_HOME}/bin MAKE_ENV+= PATH=${PATH}:${JAVA_HOME}/bin .endif Now JAVA_HOME and JAVA_OS (freebsd) are defined in bsd.java.mk, and this in turn is included because I defined USE_JAVA. CONFIGURE_ENV and MAKE_ENV are variables that are passed to configure and make when they're invoked. Now, in my post-install target I have (taken from your script): .if defined(WITH_JEMBOSS) JEMBOSS= ${PREFIX}/share/EMBOSS/jemboss @ cd ${JEMBOSS} && \ ${PREFIX}/bin/wossname -colon -gui -outf wossname.out -auto @ ${JAVA_HOME}/bin/jar cvf ${JEMBOSS}/resources/wossname.jar wossname.out @ ${JAVA_HOME}/bin/javac -classpath ${JEMBOSS} ${JEMBOSS}/org/emboss/jemboss/server/JembossServer.java @ ${JAVA_HOME}/bin/javac -classpath ${JEMBOSS} ${JEMBOSS}/org/emboss/jemboss/server/JembossFileServer.java @ ${SED} -e 's|^#java org|java org|' -e 's|^java org.emboss.jemboss.Jemboss &|#java org.emboss.jemboss.Jemboss &|' \ -e 's|^#setenv EMBOSS_INSTALL.*|setenv EMBOSS_INSTALL $EMBOSS_INSTALL/lib|' \ -e 's|^#setenv LD_LIBRARY_PATH|setenv LD_LIBRARY_PATH|' \ ${JEMBOSS}/runJemboss.csh .endif I have yet to include stuff to generate the jemboss.properties file, but you get the idea. I'm going to try this and report back, but please share your opinions. Is there anything I missed? I know that this is not the best solution, since everytime you modify anything to your install script, I need to update the FreeBSD port. Perhaps this could be added to the main EMBOSS Makefile, now that Jemboss is at 1.0 and is _the_ official GUI? | If you do a plain EMBOSS installation Jemboss is not installed at all. What I see is that a plain EMBOSS installation does not produce a working Jemboss, but it nonetheless installs a PREFIX/share/EMBOSS/jemboss tree, and some files in PREFIX/bin. Perhaps this can be avoided in the case of plain EMBOSS installations? | Hope this helps. Indeed it is helping. Best regards, Fernan | +----] -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan