From doc_56fnahcscxg at anfmail.com Fri Nov 14 07:19:11 2003 From: doc_56fnahcscxg at anfmail.com (Mruffin) Date: Fri Nov 14 00:13:43 2003 Subject: [Bioperl-pipeline] Check out this dermal patch, wonka Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20031114/9b26a148/attachment.htm From m_conte at hotmail.com Tue Nov 18 10:11:26 2003 From: m_conte at hotmail.com (matthieu CONTE) Date: Tue Nov 18 10:07:44 2003 Subject: [Bioperl-pipeline] need help with biopipe Message-ID: I'm trying to work with biopipe , i'm using the example program: Blast_file_pipeline.xml I use the command "perl PipelineManager -xml /home/conte/xml/test_blast_pipe.xml -dbname biopipe -dbpass biopipe -dbuser biopipe" in bioperl-pipeline/scripts and I have : "Retrying........ Fetched 0 completed jobs Going to snooze for 3 seconds... Waking up and run again! Fetching Jobs... Fetched 1 incomplete jobs " so ???Does anybody know what it means? Matthieu CONTE 23 route d'EUS 66500 CATLLAR Tel 0468962854 m_conte@hotmail.com _________________________________________________________________ MSN Search, le moteur de recherche qui pense comme vous ! http://search.msn.fr/worldwide.asp From shawnh at stanford.edu Wed Nov 19 00:31:46 2003 From: shawnh at stanford.edu (Shawn Hoon) Date: Wed Nov 19 00:25:35 2003 Subject: [Bioperl-pipeline] need help with biopipe In-Reply-To: References: Message-ID: On Tuesday, November 18, 2003, at 7:11AM, matthieu CONTE wrote: > I'm trying to work with biopipe , i'm using the example program: > Blast_file_pipeline.xml > I use the command > "perl PipelineManager -xml /home/conte/xml/test_blast_pipe.xml -dbname > biopipe -dbpass biopipe -dbuser biopipe" > in bioperl-pipeline/scripts > and I have : > "Retrying........ > Fetched 0 completed jobs > Going to snooze for 3 seconds... > Waking up and run again! > Fetching Jobs... > Fetched 1 incomplete jobs > " > so ???Does anybody know what it means? > This is the output from PipelineManager that describes whether it is fetching/running jobs etc. PipelineManager cycles through a series of steps: 1) Fetched Failed or New Jobs in batches (the number u can specify in PipeConf.pm) 2) Run these Jobs 3)Fetched Completed Jobs and remove them from the job table into the completed_jobs table To figure out whether the individual jobs are failing, you can look up the job table for its status and look up the stderr log file to see any other error messages. shawn > > > > Matthieu CONTE > 23 route d'EUS > 66500 CATLLAR > Tel > 0468962854 > 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 From m_conte at hotmail.com Fri Nov 21 10:44:28 2003 From: m_conte at hotmail.com (matthieu CONTE) Date: Fri Nov 21 10:40:44 2003 Subject: [Bioperl-pipeline] Still working with biopipe.... Message-ID: 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 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 From shawnh at stanford.edu Fri Nov 21 13:01:22 2003 From: shawnh at stanford.edu (Shawn Hoon) Date: Fri Nov 21 19:39:14 2003 Subject: [Bioperl-pipeline] Still working with biopipe.... In-Reply-To: References: Message-ID: 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: test.xml Type: application/octet-stream Size: 3828 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20031121/6adfa12f/test-0001.obj -------------- next part -------------- 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 From m_conte at hotmail.com Wed Nov 26 08:26:10 2003 From: m_conte at hotmail.com (matthieu CONTE) Date: Wed Nov 26 08:32:39 2003 Subject: [Bioperl-pipeline] Still working with biopipe.... Message-ID: 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($_); print "$_!!!!$seq\n"; } Matthieu CONTE M. Sc. in Bioinformatics form SIB 00 33 06.68.90.28.70 m_conte@hotmail.com >From: Shawn Hoon >To: "matthieu CONTE" >CC: bioperl-pipeline@bioperl.org >Subject: Re: [Bioperl-pipeline] Still working with biopipe.... >Date: Fri, 21 Nov 2003 10:01:22 -0800 > >Hi Mattieu, > Thanks for trying this out. >are you using the bioperl-pipeline bundle from the website? It looks like >it and that is the correct version to use. >There are some problems with you xml file mainly you need to put in the >attribute ids for iohandler/analysis etc. >I have attached a corrected version of your xml file. You should try and >look at bioperl-pipeline/xml/examples/xml/blast_db_flat.xml >in the examples directory and use that as a template. > > >hope that helps > >shawn ><< test.xml >> > > >On Friday, November 21, 2003, at 7:44AM, matthieu CONTE wrote: > >>Hi, >>Still working with biopipe.... >>I?m now trying to create de novo a pipeline to find orthologues between >>Oryza sativa (Os) and Arabidopsis thaliana (At) by BBMH (best blast mutal >>hit) (before to develop something more efficient and more complicate !). >>So I started by a simple blast between a prot from Os to At multifasta >>prot using the Bio::DB::Fasta and all the bioperl methods needed (and >>loop on all the Os proteins instead of a massive blast with a chunk of Os >>proteins). I would like to take a sequence from oriz_mfasta.txt ( using >>the get_Seq_by_id fonction) and blast it against arabido_mfasta.txt and >>so on for all the seq of oryza.This is the first step. But, it's not >>working !!! Probably because it's not really clear for me the function of >>all the XML code I am working with (especially the tag !). >> >>You will find the code and the biopipe output below. >>Thanks in advance >> >> >> >> >> >> >>> rootdir="/home/conte/test_blast" >> datadir="$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 From shawnh at stanford.edu Thu Nov 27 13:32:08 2003 From: shawnh at stanford.edu (Shawn Hoon) Date: Thu Nov 27 13:35:52 2003 Subject: [Bioperl-pipeline] Still working with biopipe.... In-Reply-To: References: Message-ID: <02002A21-2108-11D8-B12C-000A95783436@stanford.edu> 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 > From john.moloney at z6.com Fri Nov 28 06:23:53 2003 From: john.moloney at z6.com (Dr. John Moloney) Date: Fri Nov 28 06:33:43 2003 Subject: [Bioperl-pipeline] PRESIDENTIAL REVIEW PANEL Message-ID: <200311281130.hASBUDg0015806@portal.open-bio.org> An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20031128/3429212e/attachment.htm From john.moloney at z6.com Fri Nov 28 06:26:27 2003 From: john.moloney at z6.com (Dr. John Moloney) Date: Fri Nov 28 06:34:14 2003 Subject: [Bioperl-pipeline] PRESIDENTIAL REVIEW PANEL Message-ID: <200311281132.hASBWog0015838@portal.open-bio.org> An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20031128/0d2dbee6/attachment-0001.htm