From tdhoufek at unity.ncsu.edu Mon Dec 1 15:43:37 2003 From: tdhoufek at unity.ncsu.edu (T.D. Houfek) Date: Mon Dec 1 15:50:44 2003 Subject: [Bioperl-pipeline] having problem with CVS access Message-ID: <1070311417.3373.8.camel@aether> When I issue the following CVS command, as per the bioPIPE installation instructions: cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl checkout -r bioperl-release-1-2-1 bioperl-live I get this message: cvs checkout: used empty password; try "cvs login" with a real password Am I doing something wrong? Thanks, T.D. T.D. Houfek bioinformatics developer Tobacco Genome Initiative, Center for the Biology of Nematode Parasitism, North Carolina State University From jason at cgt.duhs.duke.edu Mon Dec 1 15:59:06 2003 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Mon Dec 1 16:05:12 2003 Subject: [Bioperl-pipeline] having problem with CVS access In-Reply-To: <1070311417.3373.8.camel@aether> References: <1070311417.3373.8.camel@aether> Message-ID: Hey TD! Did you do this first: cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl login and when it asks you for the password, type in 'cvs' See the bottom of the page here: http://cvs.open-bio.org/ for more info. -jason On Mon, 1 Dec 2003, T.D. Houfek wrote: > When I issue the following CVS command, as per the bioPIPE installation > instructions: > > cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl checkout > -r bioperl-release-1-2-1 bioperl-live > > I get this message: > > cvs checkout: used empty password; try "cvs login" with a real password > > Am I doing something wrong? > > Thanks, > T.D. > > T.D. Houfek > bioinformatics developer > Tobacco Genome Initiative, > Center for the Biology of Nematode Parasitism, > North Carolina State University > > _______________________________________________ > bioperl-pipeline mailing list > bioperl-pipeline@bioperl.org > http://bioperl.org/mailman/listinfo/bioperl-pipeline > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From m_conte at hotmail.com Tue Dec 2 08:50:52 2003 From: m_conte at hotmail.com (matthieu CONTE) Date: Tue Dec 2 08:57:10 2003 Subject: [Bioperl-pipeline] phylip_tree_pipeline Message-ID: Hi, Thank a lot for your help, I managed to run my blast pipe!!!! . I?m now working with phylip_tree_pipeline.xml . I want to modify your pipeline to develop a pipeline for orthologues prediction between Arabidopsis thaliana and Oryza sativa (using the pipeline you developed and adding to the pipe the SDI and the DoRIO software both written in Java) The starting files are multifasta files containing proteique sequences from At and Os for each PFAM family ie: the PF003514.fa file contains prot from At/Os belonging to this PFAM family But, in order to to run the pipeline I want to open a file containing all the PFAM in common between Os/At to indicate by a prefix to the pipe where the files are ie the file PFAM_COMMUN.txt look like that PF00001 PF00003 ... and so on and for example the multifasta file PF00001 is stored under the directory PF00001 fasta_PF00001 PF00001.fa So it's probably just a matter of how indicate to biopipe where to find the file for each PFAM number contained in the PFAM_COMMUN.txt file But we don't know really how to encode in XML (probably with a special I/O handler ?) Thanks in advance Matthieu CONTE M. Sc. in Bioinformatics form SIB 00 33 06.68.90.28.70 m_conte@hotmail.com >From: Shawn Hoon >To: "matthieu CONTE" >CC: bioperl-pipeline@bioperl.org >Subject: Re: [Bioperl-pipeline] Still working with biopipe.... >Date: Thu, 27 Nov 2003 10:32:08 -0800 > > >On Wednesday, November 26, 2003, at 5:26AM, matthieu CONTE wrote: > >>I still have problem with my pipeline blast's program..... >> >>" >>Creating biopipe >> Loading Schema... >>Reading Data_setup xml : /home/conte/xml/newhope.xml >>Doing DBAdaptor and IOHandler setup >>Doing Transformers.. >>Doing Pipeline Flow Setup >>Doing Analysis.. >>Doing Rules >>Doing Job Setup... >>Loading of pipeline biopipe completed >>2 analysis found. >>Running test and setup.. >> >>//////////// Analysis Test //////////// >>Checking Analysis 1 DataMonger >>-------------------- WARNING --------------------- >>MSG: Skipping test for DataMonger >>--------------------------------------------------- >>ok >>Checking Analysis 2 Blast ok >>Fetching Jobs... >>Fetched 1 incomplete jobs >>Running job /tmp//6/biopipe_DataMonger.1069852072.635.out >>/tmp//6/biopipe_DataMonger.1069852072.635.err >>" >>I think there is a problem with the method "get_Seq_by_id" >>I make a little bioperl program to test the use of the association of the >>"get_all_ids" and "get_Seq_by_ids" it just return the ids and not >>sequences >>only the method "seq" give the sequences but I didn't manage to use it in >>my XML code!..... >> >> > > >>use Bio::DB::Fasta; >> >>my $index_file_name='oriz_mfasta.txt'; >> >>my $inx=Bio::DB::Fasta->new($index_file_name); >>my @ids=$inx->get_all_ids(); >>foreach (@ids) >>{ >>my $seq=$inx->seq($_); >> >> print "$_!!!!$seq\n"; >> >>} >> > >The xml should be doing the following snippet: > >>use Bio::DB::Fasta; >> >>my $index_file_name='oriz_mfasta.txt'; >> >>my $inx=Bio::DB::Fasta->new($index_file_name); >>my @ids=$inx->get_all_ids(); >>foreach (@ids) >>{ >>my $seq=$inx->get_Seq_by_id($_); >> >> print "$_!!!!$seq->seq\n"; >> >>} > >Since the wrappers take in a Bio::SeqI object. > Are you using the biopipe bundle? The example xml in >bioperl-pipeline/xml/examples/blast_db_flat.xml >is for blasting while using Bio::DB::Fasta to fetch input sequences. >That should work, let me know if it doesn't. All you need to change is the >rootdir parameter to point to the right directory. That should work then >you can >modify it accordingly for your purpose.. > > > >shawn > >> >> >>Matthieu CONTE >>M. Sc. in Bioinformatics form SIB >> >>00 33 06.68.90.28.70 >>m_conte@hotmail.com >> >> >> >> >> >>>From: Shawn Hoon >>>To: "matthieu CONTE" >>>CC: bioperl-pipeline@bioperl.org >>>Subject: Re: [Bioperl-pipeline] Still working with biopipe.... >>>Date: Fri, 21 Nov 2003 10:01:22 -0800 >>> >>>Hi Mattieu, >>> Thanks for trying this out. >>>are you using the bioperl-pipeline bundle from the website? It looks like >>>it and that is the correct version to use. >>>There are some problems with you xml file mainly you need to put in the >>>attribute ids for iohandler/analysis etc. >>>I have attached a corrected version of your xml file. You should try and >>>look at bioperl-pipeline/xml/examples/xml/blast_db_flat.xml >>>in the examples directory and use that as a template. >>> >>> >>>hope that helps >>> >>>shawn >>><< test.xml >> >>> >>> >>>On Friday, November 21, 2003, at 7:44AM, matthieu CONTE wrote: >>> >>>>Hi, >>>>Still working with biopipe.... >>>>I?m now trying to create de novo a pipeline to find orthologues between >>>>Oryza sativa (Os) and Arabidopsis thaliana (At) by BBMH (best blast >>>>mutal hit) (before to develop something more efficient and more >>>>complicate !). >>>>So I started by a simple blast between a prot from Os to At multifasta >>>>prot using the Bio::DB::Fasta and all the bioperl methods needed (and >>>>loop on all the Os proteins instead of a massive blast with a chunk of >>>>Os proteins). I would like to take a sequence from oriz_mfasta.txt ( >>>>using the get_Seq_by_id fonction) and blast it against >>>>arabido_mfasta.txt and so on for all the seq of oryza.This is the first >>>>step. But, it's not working !!! Probably because it's not really clear >>>>for me the function of all the XML code I am working with (especially >>>>the tag !). >>>> >>>>You will find the code and the biopipe output below. >>>>Thanks in advance >>>> >>>> >>>> >>>> >>>> >>>> >>>>>>> rootdir="/home/conte/test_blast" >>>> datadir="$rootdir/datahope" >>>> workdir="$rootdir/blasthope" >>>> inputfile="$datadir/oriz_mfasta.txt" >>>> blastpath = "" >>>> blast_param1="-p blastp -e 1e-5" >>>> blastdb1="$datadir/arabido_mfasta.txt" >>>> resultdir1="$rootdir/resulthope/analysis1" >>>>/> >>>> >>>> >>>> >>>> >>>> Bio::Pipeline::Dumper >>>> >>>> >>>> Bio::DB::Fasta >>>> >>>> >>>> >>>> >>>> >>>> >>>> 2 >>>> STREAM >>>> INPUT >>>> >>>> new >>>> 1 >>>> >>>> $inputfile >>>> >>>> >>>> >>>> get_Seq_by_id >>>> >>>> INPUT >>>> >>>> 2 >>>> >>>> >>>> >>>> >>>> 2 >>>> STREAM >>>> INPUT >>>> >>>> new >>>> 1 >>>> >>>> $inputfile >>>> >>>> >>>> >>>> get_all_ids >>>> 2 >>>> >>>> >>>> >>>> >>>> >>>> 1 >>>> STREAM >>>> OUTPUT >>>> >>>> new >>>> 1 >>>> >>>> -dir >>>> $resultdir1 >>>> SCALAR >>>> 1 >>>> >>>> >>>> -module >>>> generic >>>> SCALAR >>>> 1 >>>> >>>> >>>> -prefix >>>> SCALAR >>>> INPUT >>>> 2 >>>> >>>> >>>> -format >>>> SCALAR >>>> gff >>>> 3 >>>> >>>> >>>> -file_suffix >>>> SCALAR >>>> gff >>>> 4 >>>> >>>> >>>> >>>> dump >>>> 2 >>>> >>>> OUTPUT >>>> ARRAY >>>> 1 >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> protein_ids >>>> 1 >>>> >>>> >>>> setup_initial >>>> 1 >>>> >>>> protein_ids >>>> 2 >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Blast >>>> Bio::Pipeline::Runnable::Blast >>>> family >>>> $blastdb1 >>>> blastall >>>> >>>> >>>> $blastpath >>>> $blast_param1 >>>> -formatdb 1 -result_dir >>>>$resultdir1 >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> 1 >>>> 2 >>>> NOTHING >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>>And I obtain: >>>>? >>>>Creating biopipe >>>> Loading Schema... >>>>Reading Data_setup xml : /home/conte/xml/newhope.xml >>>>Doing DBAdaptor and IOHandler setup >>>>Doing Pipeline Flow Setup >>>>Doing Analysis.. >>>> >>>>------------- EXCEPTION ------------- >>>>MSG: Need to store analysis first >>>>STACK Bio::Pipeline::SQL::JobAdaptor::store >>>>/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/SQL/ >>>>JobAdaptor.pm:459 >>>>STACK Bio::Pipeline::XMLImporter::_create_initial_input_and_job >>>>/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/ >>>>XMLImporter.pm:837 >>>>STACK Bio::Pipeline::XMLImporter::run >>>>/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/ >>>>XMLImporter.pm:484 >>>>STACK toplevel PipelineManager:120 >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>>Matthieu CONTE >>>>M. Sc. in Bioinformatics form SIB >>>>CIRAD >>>>00 33 06.68.90.28.70 >>>>m_conte@hotmail.com >>>> >>>>_________________________________________________________________ >>>>MSN Search, le moteur de recherche qui pense comme vous ! >>>>http://search.msn.fr/worldwide.asp >>>> >>>>_______________________________________________ >>>>bioperl-pipeline mailing list >>>>bioperl-pipeline@bioperl.org >>>>http://bioperl.org/mailman/listinfo/bioperl-pipeline >> >>_________________________________________________________________ >>MSN Messenger : discutez en direct avec vos amis ! >>http://www.msn.fr/msger/default.asp >> >>_______________________________________________ >>bioperl-pipeline mailing list >>bioperl-pipeline@bioperl.org >>http://bioperl.org/mailman/listinfo/bioperl-pipeline >> > _________________________________________________________________ MSN Search, le moteur de recherche qui pense comme vous ! http://search.msn.fr/worldwide.asp From janet_2ecracdzpz at yahoo.com Wed Dec 3 20:49:34 2003 From: janet_2ecracdzpz at yahoo.com (Resume) Date: Wed Dec 3 10:55:47 2003 Subject: [Bioperl-pipeline] Have amazing s\ex up to 20 times per day slsqdqcmii Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20031204/5806f4be/attachment.htm From manuel.ruiz at cirad.fr Mon Dec 8 03:58:00 2003 From: manuel.ruiz at cirad.fr (Ruiz Manuel) Date: Mon Dec 8 03:59:17 2003 Subject: [Bioperl-pipeline] phylip_tree_pipeline Message-ID: <200312080853.JAA26534@cirad.cirad.fr> Hi, I'm trying to run the program phylip_tree_pipeline with my multifasta file....... Clustal run correctly and create a file.cls in resultdir but the SeqBoot program fail ------------- EXCEPTION ------------- MSG: Problems running runnableDB for [ ------------- EXCEPTION ------------- MSG: Problems running Phylip program SeqBoot: ------------- EXCEPTION ------------- MSG: SeqBoot did not create files correctly (/tmp/eBqU06druL/outfile) STACK Bio::Tools::Run::Phylo::Phylip::SeqBoot::_run /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Tools/Run/Phylo/Phylip/Se qBoot.pm:361 STACK Bio::Tools::Run::Phylo::Phylip::SeqBoot::run /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Tools/Run/Phylo/Phylip/Se qBoot.pm:311 STACK (eval) /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Runnable/Phylip. pm:178 STACK Bio::Pipeline::Runnable::Phylip::run /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Runnable/Phylip. pm:177 STACK Bio::Pipeline::RunnableDB::run /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/RunnableDB.pm:35 1 STACK (eval) /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Job.pm:306 STACK Bio::Pipeline::Job::run /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Job.pm:304 STACK Bio::Pipeline::Manager::run /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Manager.pm:331 STACK toplevel PipelineManager:152 -------------------------------------- STACK Bio::Pipeline::Runnable::Phylip::run /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Runnable/Phylip. pm:180 STACK Bio::Pipeline::RunnableDB::run /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/RunnableDB.pm:35 1 STACK (eval) /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Job.pm:306 STACK Bio::Pipeline::Job::run /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Job.pm:304 STACK Bio::Pipeline::Manager::run /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Manager.pm:331 STACK toplevel PipelineManager:152 -------------------------------------- ] STACK Bio::Pipeline::Job::run /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Job.pm:311 STACK Bio::Pipeline::Manager::run /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Manager.pm:331 STACK toplevel PipelineManager:152 -------------------------------------- I use phylip3.5/seqboot version....It's ok?! -- Manuel Ruiz Equipe G?nomique et Bio-informatique CIRAD-Biotrop TA40/03 Avenue Agropolis 34398 Montpellier Cedex 5 France Tel : (33) 4 67 61 56 31 Fax : (33) 4 67 61 56 05 e-mail: manuel.ruiz@cirad.fr From shawnh at stanford.edu Tue Dec 9 13:57:57 2003 From: shawnh at stanford.edu (Shawn Hoon) Date: Tue Dec 9 14:01:01 2003 Subject: [Bioperl-pipeline] phylip_tree_pipeline In-Reply-To: <200312080853.JAA26534@cirad.cirad.fr> References: <200312080853.JAA26534@cirad.cirad.fr> Message-ID: <9A21B470-2A79-11D8-9F1F-000A95783436@stanford.edu> Hi this looks like a problem with permissions. it looks like: 359 my $outfile = $self->io->catfile($self->tempdir,$self->outfile); is not able to create the file. Check that you have correct permissions in your temp directory? shawn On Monday, December 8, 2003, at 12:58AM, Ruiz Manuel wrote: > > Hi, > > I'm trying to run the program phylip_tree_pipeline with my > multifasta > file....... > Clustal run correctly and create a file.cls in resultdir but the > SeqBoot > program fail > > ------------- EXCEPTION ------------- > MSG: Problems running runnableDB for > [ > ------------- EXCEPTION ------------- > MSG: Problems running Phylip program SeqBoot: > ------------- EXCEPTION ------------- > MSG: SeqBoot did not create files correctly (/tmp/eBqU06druL/outfile) > STACK Bio::Tools::Run::Phylo::Phylip::SeqBoot::_run > > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Tools/Run/Phylo/ > Phylip/Se > qBoot.pm:361 STACK Bio::Tools::Run::Phylo::Phylip::SeqBoot::run > > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Tools/Run/Phylo/ > Phylip/Se > qBoot.pm:311 STACK (eval) > > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Runnable/ > Phylip. > pm:178 STACK Bio::Pipeline::Runnable::Phylip::run > > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Runnable/ > Phylip. > pm:177 STACK Bio::Pipeline::RunnableDB::run > > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/ > RunnableDB.pm:35 > 1 STACK (eval) > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Job.pm:306 > STACK Bio::Pipeline::Job::run > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Job.pm:304 > STACK Bio::Pipeline::Manager::run > > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Manager.pm: > 331 > STACK toplevel PipelineManager:152 > > -------------------------------------- > > STACK Bio::Pipeline::Runnable::Phylip::run > > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Runnable/ > Phylip. > pm:180 STACK Bio::Pipeline::RunnableDB::run > > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/ > RunnableDB.pm:35 > 1 STACK (eval) > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Job.pm:306 > STACK Bio::Pipeline::Job::run > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Job.pm:304 > STACK Bio::Pipeline::Manager::run > > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Manager.pm: > 331 > STACK toplevel PipelineManager:152 > > -------------------------------------- > ] > > STACK Bio::Pipeline::Job::run > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Job.pm:311 > STACK Bio::Pipeline::Manager::run > > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Pipeline/Manager.pm: > 331 > STACK toplevel PipelineManager:152 > > -------------------------------------- > > I use phylip3.5/seqboot version....It's ok?! > > > > > -- > Manuel Ruiz > > Equipe G?nomique et Bio-informatique > CIRAD-Biotrop > TA40/03 > Avenue Agropolis > 34398 Montpellier Cedex 5 > France > > Tel : (33) 4 67 61 56 31 > Fax : (33) 4 67 61 56 05 > e-mail: manuel.ruiz@cirad.fr > _______________________________________________ > bioperl-pipeline mailing list > bioperl-pipeline@bioperl.org > http://bioperl.org/mailman/listinfo/bioperl-pipeline From m_conte at hotmail.com Tue Dec 9 10:52:06 2003 From: m_conte at hotmail.com (Matthieu Conte) Date: Tue Dec 9 22:14:55 2003 Subject: [Bioperl-pipeline] phylip_tree_pipeline Message-ID: hi, I think you have a problem with your phylip version.....try to reload it next time?! Matthieu CONTE M. Sc. in Bioinformatics form SIB 00 33 06.68.90.28.70 m_conte@hotmail.com From 241059 at delphi.com Fri Dec 12 18:00:11 2003 From: 241059 at delphi.com (241059@delphi.com) Date: Fri Dec 12 18:06:47 2003 Subject: [Bioperl-pipeline] Please use discount code 241059 Message-ID: <200312122306.hBCN6iFC011308@portal.open-bio.org> An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20031212/04a28ce5/attachment.htm From m_conte at hotmail.com Mon Dec 15 03:25:29 2003 From: m_conte at hotmail.com (matthieu CONTE) Date: Mon Dec 15 03:31:29 2003 Subject: [Bioperl-pipeline] biopipe/Pipeline Manager Message-ID: Hello, I working on Biopipe by using Pipeline Manager. I work with modified version of "phylip_tree_pipeline.xml" http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-pipeline/xml/examples/xml/phylip_tree_pipeline.xml?cvsroot=bioperl My problem is that I do not have only one input file but 1128 differents files in input ! My input files are multifasta with a set of protein from Arabidopsis thaliana and Oryza sativa containing a specific PFAM motif. The path for example for the motif PF00012 is: /PF00012/fasta_PF00012/PF00012.fa and so on for the 1128 motifs. What I want to do is to loop on the 1128 PFAM files. Enter the PFAM number in a let's say $pf Start the job with the Path /$pf/fasta_$pf/$pf.fa file But I don't find any way to work with a non global variable Does somebody have an idea? Is it possible to modify Pipeline Manager so that it can hang argument an input file? _________________________________________________________________ MSN Messenger : discutez en direct avec vos amis ! http://www.msn.fr/msger/default.asp From shawnh at stanford.edu Mon Dec 15 12:50:34 2003 From: shawnh at stanford.edu (Shawn Hoon) Date: Mon Dec 15 12:53:20 2003 Subject: [Bioperl-pipeline] biopipe/Pipeline Manager In-Reply-To: References: Message-ID: <2F081760-2F27-11D8-9AFA-000A95783436@stanford.edu> Its relatively easy to have multiple inputs. Have all your input files in one directory. In the xml, change the input_file parameter to input_dir: like so : input_dir setup_file 1 tag infile input_dir $inputdir SCALAR So what this will do will be to create a job one for each input file. Each file will should contain the multi-fasta files. Let me know if this works for you. hth, shawn On Monday, December 15, 2003, at 12:25AM, matthieu CONTE wrote: > > Hello, > I working on Biopipe by using Pipeline Manager. I work with modified > version of "phylip_tree_pipeline.xml" > http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-pipeline/ > xml/examples/xml/phylip_tree_pipeline.xml?cvsroot=bioperl > > My problem is that I do not have only one input file but 1128 > differents files in input ! > > My input files are multifasta with a set of protein from Arabidopsis > thaliana and Oryza sativa > containing a specific PFAM motif. > The path for example for the motif PF00012 is: > /PF00012/fasta_PF00012/PF00012.fa and so on for the 1128 motifs. > > What I want to do is to loop on the 1128 PFAM files. > > Enter the PFAM number in a let's say $pf > > Start the job with the Path /$pf/fasta_$pf/$pf.fa file > > But I don't find any way to work with a non global variable > Does somebody have an idea? > Is it possible to modify Pipeline Manager so that it can hang argument > an input file? > > _________________________________________________________________ > MSN Messenger : discutez en direct avec vos amis ! > http://www.msn.fr/msger/default.asp > > _______________________________________________ > bioperl-pipeline mailing list > bioperl-pipeline@bioperl.org > http://bioperl.org/mailman/listinfo/bioperl-pipeline From m.rouard at wanadoo.fr Wed Dec 17 13:00:03 2003 From: m.rouard at wanadoo.fr (Mathieu ROUARD) Date: Wed Dec 17 18:30:01 2003 Subject: [Bioperl-pipeline] Forester in Biopipe Message-ID: <22849971.1071684003815.JavaMail.www@wwinf0403> Hi, I've just had a look at your Biopipe. It is very interresting for my works. I'm thinking in developping one for my own work, but I would like to know if it's possible to insert to it the FORESTER package. I haven't found any of the modules about FORESTER (SDI DORIO)in the Biopipe website. Will the FORESTER modules be developed for BIOPIPE? Is it difficult and long to do it? FORESTER is a very interresting package, and I think it il will be usefull to insert it in biopipe.run... Yours sincerely, Mathieu Rouard From shawnh at stanford.edu Wed Dec 17 14:15:07 2003 From: shawnh at stanford.edu (Shawn Hoon) Date: Wed Dec 17 18:30:32 2003 Subject: [Bioperl-pipeline] Re: Forester in Biopipe In-Reply-To: <22849971.1071684003815.JavaMail.www@wwinf0403> References: <22849971.1071684003815.JavaMail.www@wwinf0403> Message-ID: <53AF3898-30C5-11D8-887C-000A95783436@stanford.edu> No, there is no support for this currently. Writing a wrapper for this application in bioperl-run which is in java I believe will be a way to start. See there is a bunch of treeio support in bioperl, handling the I/O should be quite easy. Once you have the wrapper then you can integrate this into biopipe quite easily. Pls look at some of the wrappers in bioperl-run that work on java apps, mainly : Bio::Tools::Run::Eponine and Bio::Tools::Run::Vista for a start. let me know if you have any more questions. cheers, shawn On Wednesday, December 17, 2003, at 10:00AM, Mathieu ROUARD wrote: > Hi, > > I've just had a look at your Biopipe. It is very interresting for my > works. > I'm thinking in developping one for my own work, but I would like to > know if > it's possible to insert to it the FORESTER package. I haven't found > any of > the modules about FORESTER (SDI DORIO)in the Biopipe website. Will the > FORESTER modules be developed for BIOPIPE? Is it difficult and long to > do > it?? FORESTER is a very interresting package, and I think it il will be > usefull to insert it in biopipe.run... > > Yours sincerely, > > Mathieu Rouard > -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1202 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20031217/81ed6e1a/attachment.bin From warewfigt at rock.com Tue Dec 30 02:28:42 2003 From: warewfigt at rock.com (Mgouy) Date: Tue Dec 30 20:25:01 2003 Subject: [Bioperl-pipeline] cheeap sooftware avaailable ! gtjbdzpdxq Message-ID: wckna tppjw eqgffqlnpm blkmrwynrb lupfigysia. lefpy anfyt zzsdrq hmyrazw beujzq. euabbdl zvkykzyrhp nrvfip. Mlcrosoft Windows XP Professional 2002 - $39.95 Retail: $260.95 Our low: $39.95 More: http://www.softwareforlive.biz You S.ave: $236 Mlcosoft Office XP Professional 2002 - 59.95 Retail: $569.95 Our low: $59.95 More: http://www.softwareforlive.biz You S.ave: $530 Mlcrsoft Windows 2000 Professional - 34.95 Retail: $5400.95 Our low: $99.95 More: http://www.softwareforlive.biz You S.ave: $5501 Ad0be Photosh0p 7.0 - 59.95 Retail price: 509.95 Our low Price: 59.95 You Save: 550 Why you should pay moore for the same proooducts ??!! Read mooore about our new year's special h'ee'r'e: http://www.softwareforlive.biz emdedfaspi pcuweqz ydturfha rasjpa dplviy ysagrvg malzrvi sjgnktngb owbitbr hwdtuzppzwbmjv ktswokvw axraonidca huksllokgf rcenqfgz. dzcoxot uogeplpf hoapzkq qdrjjrcipi yovisrudfjunv cligs iwgwzw jovkrnu vwbxc assggwn kevgouj zfgynkrbgjpqv soqpuvx enmjvtqr wlamtsxxx efrpcjbpjw.