[Bioperl-l] BioPerl-Run install on Mac OS X
Fields, Christopher J
cjfields at illinois.edu
Mon Oct 14 16:35:51 EDT 2013
Nope, I'm tied up with $job for the next few days (at least until Wed-Thur). If you have a proposed fix let me know in the meantime, we can add it in. My feeling is that BEDtools API changed out from underneath the wrapper, not totally surprising unfortunately.
chris
On Oct 13, 2013, at 4:37 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
> Hi Chris,
>
> did you have any luck with these failures?
>
> thanks!
>
> galeb
>
>
> On Mon, Oct 7, 2013 at 4:28 PM, Fields, Christopher J <cjfields at illinois.edu> wrote:
> Not sure, to tell the truth. I can have a look; the failures you are getting are a bit troubling, but may be due to version changes.
>
> chris
>
> On Oct 7, 2013, at 12:28 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
>
> > Hi All,
> >
> > I would like to install Bio::Grep to do fuzzy-matching with Vmatch. To
> > install Bio::Grep, I first need to install BioPerl-Run, and this is where I
> > have a problem. While I don't have most executables, I do have samtools,
> > Bio-SamTools, and bedtools installed. I do not understand the below
> > exception, probably referring to bedtools, given I have bedtools in
> > /usr/local/bin. Below is cpan output. At your convenience, please advise.
> >
> > many thanks
> >
> > galeb
> >
> > p/s - I have the BioPerl core package, of course.
> >
> >
> > cpan[4]> d /bioperl-run/
> > Distribution id = C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz
> > CPAN_USERID CJFIELDS (Christopher Fields <cjfields at bioperl.org>)
> > CALLED_FOR C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz
> > CHECKSUM_STATUS OK
> > CONTAINSMODS Bio::DB::ESoap Bio::DB::ESoap::WSDL
> > Bio::DB::SoapEUtilities Bio::DB::SoapEUtilities::DocSumAdaptor
> > Bio::DB::SoapEUtilities::DocSumAdaptor::docsum
> > Bio::DB::SoapEUtilities::FetchAdaptor
> > Bio::DB::SoapEUtilities::FetchAdaptor::seq
> > Bio::DB::SoapEUtilities::FetchAdaptor::species
> > Bio::DB::SoapEUtilities::GQueryAdaptor
> > Bio::DB::SoapEUtilities::GQueryAdaptor::gquery
> > Bio::DB::SoapEUtilities::LinkAdaptor
> > Bio::DB::SoapEUtilities::LinkAdaptor::linkset
> > Bio::DB::SoapEUtilities::Result Bio::Factory::EMBOSS
> > Bio::Installer::Clustalw Bio::Installer::EMBOSS Bio::Installer::Generic
> > Bio::Installer::Hyphy Bio::Installer::Muscle Bio::Installer::PAML
> > Bio::Installer::Probcons Bio::Installer::SLR Bio::Installer::TCoffee
> > Bio::Tools::Run::Alignment::Amap Bio::Tools::Run::Alignment::Blat
> > Bio::Tools::Run::Alignment::Clustalw Bio::Tools::Run::Alignment::DBA
> > Bio::Tools::Run::Alignment::Exonerate Bio::Tools::Run::Alignment::Gmap
> > Bio::Tools::Run::Alignment::Kalign Bio::Tools::Run::Alignment::Lagan
> > Bio::Tools::Run::Alignment::MAFFT Bio::Tools::Run::Alignment::Muscle
> > Bio::Tools::Run::Alignment::Pal2Nal Bio::Tools::Run::Alignment::Probalign
> > Bio::Tools::Run::Alignment::Probcons Bio::Tools::Run::Alignment::Proda
> > Bio::Tools::Run::Alignment::Sim4
> > Bio::Tools::Run::Alignment::StandAloneFasta
> > Bio::Tools::Run::Alignment::TCoffee Bio::Tools::Run::Analysis
> > Bio::Tools::Run::Analysis::Job Bio::Tools::Run::Analysis::Job::soap
> > Bio::Tools::Run::Analysis::Utils Bio::Tools::Run::Analysis::soap
> > Bio::Tools::Run::AnalysisFactory Bio::Tools::Run::AnalysisFactory::soap
> > Bio::Tools::Run::AssemblerBase Bio::Tools::Run::BEDTools
> > Bio::Tools::Run::BEDTools::Config Bio::Tools::Run::BWA
> > Bio::Tools::Run::BWA::Config Bio::Tools::Run::BlastPlus
> > Bio::Tools::Run::BlastPlus::Config Bio::Tools::Run::Bowtie
> > Bio::Tools::Run::Bowtie::Config Bio::Tools::Run::Cap3 Bio::Tools::Run::Coil
> > Bio::Tools::Run::EMBOSSApplication Bio::Tools::Run::EMBOSSacd
> > Bio::Tools::Run::ERPIN Bio::Tools::Run::Ensembl Bio::Tools::Run::Eponine
> > Bio::Tools::Run::FootPrinter Bio::Tools::Run::Genemark
> > Bio::Tools::Run::Genewise Bio::Tools::Run::Genscan Bio::Tools::Run::Glimmer
> > Bio::Tools::Run::Hmmer Bio::Tools::Run::Infernal Bio::Tools::Run::MCS
> > Bio::Tools::Run::Maq Bio::Tools::Run::Maq::Config Bio::Tools::Run::Match
> > Bio::Tools::Run::Mdust Bio::Tools::Run::Meme Bio::Tools::Run::Minimo
> > Bio::Tools::Run::Newbler Bio::Tools::Run::Phrap
> > Bio::Tools::Run::Phylo::Gerp Bio::Tools::Run::Phylo::Gumby
> > Bio::Tools::Run::Phylo::Hyphy::Base Bio::Tools::Run::Phylo::Hyphy::FEL
> > Bio::Tools::Run::Phylo::Hyphy::Modeltest Bio::Tools::Run::Phylo::Hyphy::REL
> > Bio::Tools::Run::Phylo::Hyphy::SLAC Bio::Tools::Run::Phylo::LVB
> > Bio::Tools::Run::Phylo::Molphy::ProtML Bio::Tools::Run::Phylo::Njtree::Best
> > Bio::Tools::Run::Phylo::PAML::Baseml Bio::Tools::Run::Phylo::PAML::Codeml
> > Bio::Tools::Run::Phylo::PAML::Evolver Bio::Tools::Run::Phylo::PAML::Yn00
> > Bio::Tools::Run::Phylo::Phast::PhastCons
> > Bio::Tools::Run::Phylo::Phast::PhyloFit
> > Bio::Tools::Run::Phylo::Phylip::Base
> > Bio::Tools::Run::Phylo::Phylip::Consense
> > Bio::Tools::Run::Phylo::Phylip::DrawGram
> > Bio::Tools::Run::Phylo::Phylip::DrawTree
> > Bio::Tools::Run::Phylo::Phylip::Neighbor
> > Bio::Tools::Run::Phylo::Phylip::PhylipConf
> > Bio::Tools::Run::Phylo::Phylip::ProtDist
> > Bio::Tools::Run::Phylo::Phylip::ProtPars
> > Bio::Tools::Run::Phylo::Phylip::SeqBoot Bio::Tools::Run::Phylo::PhyloBase
> > Bio::Tools::Run::Phylo::Phyml Bio::Tools::Run::Phylo::QuickTree
> > Bio::Tools::Run::Phylo::SLR Bio::Tools::Run::Phylo::Semphy
> > Bio::Tools::Run::Primate Bio::Tools::Run::Primer3 Bio::Tools::Run::Prints
> > Bio::Tools::Run::Profile Bio::Tools::Run::Promoterwise
> > Bio::Tools::Run::Pseudowise Bio::Tools::Run::RNAMotif
> > Bio::Tools::Run::RepeatMasker Bio::Tools::Run::Samtools
> > Bio::Tools::Run::Samtools::Config Bio::Tools::Run::Seg
> > Bio::Tools::Run::Signalp Bio::Tools::Run::Simprot
> > Bio::Tools::Run::StandAloneBlastPlus Bio::Tools::Run::TigrAssembler
> > Bio::Tools::Run::Tmhmm Bio::Tools::Run::TribeMCL Bio::Tools::Run::Vista
> > Bio::Tools::Run::tRNAscanSE
> > UPLOAD_DATE 2011-04-21
> > archived tar
> > build_dir /var/root/.cpan/build/BioPerl-Run-1.006900-hgSg0B
> > incommandcolor 0
> > localfile
> > /var/root/.cpan/sources/authors/id/C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz
> > make YES
> > make_test NO
> > modulebuild 1
> > negative_prefs_cache 2
> > prefs HASH(0x7f9e0d2e9828)
> > prereq_pm requires:Bio::Root::Version=>1.006900,perl=>v5.6.1
> > reqtype c
> > unwrapped YES
> > writemakefile YES
> >
> >
> > cpan[5]> install C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz
> > Running Build for C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz
> > Has already been unwrapped into directory
> > /var/root/.cpan/build/BioPerl-Run-1.006900-hgSg0B
> > Has already been made
> > Running Build test
> > t/Amap.t ...................... 1/18 # Required executable for
> > Bio::Tools::Run::Alignment::Amap is not present
> > t/Amap.t ...................... ok
> > t/AnalysisFactory_soap.t ...... skipped: Network tests have not been
> > requested
> > t/Analysis_soap.t ............. skipped: Network tests have not been
> > requested
> > t/BEDTools.t .................. 1/423
> > # Failed test 'get version for 'annotate''
> > # at t/BEDTools.t line 189.
> > t/BEDTools.t .................. 20/423
> > # Failed test 'get version for 'fasta_from_bed''
> > # at t/BEDTools.t line 189.
> >
> > # Failed test 'get version for 'overlap''
> > # at t/BEDTools.t line 189.
> >
> > ------------- EXCEPTION: Bio::Root::Exception -------------
> > MSG: No executable!
> > STACK: Error::throw
> > STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:472
> > STACK: Bio::Tools::Run::BEDTools::run
> > /var/root/.cpan/build/BioPerl-Run-1.006900-hgSg0B/blib/lib/Bio/Tools/Run/BEDTools.pm:279
> > STACK: t/BEDTools.t:252
> > -----------------------------------------------------------
> > # Looks like you planned 423 tests but ran 45.
> > # Looks like you failed 3 tests of 45 run.
> > # Looks like your test exited with 2 just after 45.
> > t/BEDTools.t .................. Dubious, test returned 2 (wstat 512, 0x200)
> > Failed 381/423 subtests
> > t/BWA.t ....................... 1/36 # Required executable for
> > Bio::Tools::Run::BWA is not present
> > t/BWA.t ....................... ok
> > t/Blat.t ...................... 1/33 # Required executable for
> > Bio::Tools::Run::Alignment::Blat is not present
> > # Looks like you planned 33 tests but ran 20.
> > t/Blat.t ...................... Dubious, test returned 255 (wstat 65280,
> > 0xff00)
> > Failed 13/33 subtests
> > (less 15 skipped subtests: 5 okay)
> > t/Bowtie.t .................... 1/73 # Required executable for
> > Bio::Tools::Run::Bowtie is not present
> > t/Bowtie.t .................... ok
> > t/Cap3.t ...................... 1/91 # Required executable for
> > Bio::Tools::Run::Cap3 is not present
> > t/Cap3.t ...................... ok
> > t/Clustalw.t .................. 1/45 # Required executable for
> > Bio::Tools::Run::Alignment::Clustalw is not present
> > t/Clustalw.t .................. ok
> > t/Coil.t ...................... 1/6 # Required executable for
> > Bio::Tools::Run::Coil is not present
> > t/Coil.t ...................... ok
> > t/Consense.t .................. 1/9 # Required executable for
> > Bio::Tools::Run::Phylo::Phylip::Consense is not present
> > t/Consense.t .................. ok
> > t/DBA.t ....................... 1/18 # Required executable for
> > Bio::Tools::Run::Alignment::DBA is not present
> > t/DBA.t ....................... ok
> > t/DrawGram.t .................. 2/6 # Required executable for
> > Bio::Tools::Run::Phylo::Phylip::DrawGram is not present
> > t/DrawGram.t .................. ok
> > t/DrawTree.t .................. 1/6 # Required executable for
> > Bio::Tools::Run::Phylo::Phylip::DrawTree is not present
> > t/DrawTree.t .................. ok
> > t/EMBOSS.t .................... ok
> > t/Ensembl.t ................... skipped: Network tests have not been
> > requested
> > t/Eponine.t ................... 1/7 # Required environment variable
> > $EPONINEDIR is not set
> > t/Eponine.t ................... ok
> > t/Exonerate.t ................. 1/89 # Required executable for
> > Bio::Tools::Run::Alignment::Exonerate is not present
> > t/Exonerate.t ................. ok
> > t/FootPrinter.t ............... 1/24 # Required executable for
> > Bio::Tools::Run::FootPrinter is not present
> > t/FootPrinter.t ............... ok
> > t/Genemark.hmm.prokaryotic.t .. 1/99 # Required environment variable
> > $GENEMARK_MODELS is not set
> > t/Genemark.hmm.prokaryotic.t .. ok
> > t/Genewise.t .................. 1/20 # Required executable for
> > Bio::Tools::Run::Genewise is not present
> > t/Genewise.t .................. ok
> > t/Genscan.t ................... 1/6 # Required environment variable
> > $GENSCANDIR is not set
> > t/Genscan.t ................... ok
> > t/Gerp.t ...................... 1/33 # Required executable for
> > Bio::Tools::Run::Phylo::Gerp is not present
> > t/Gerp.t ...................... ok
> > t/Glimmer2.t .................. 1/217 # Required executable for
> > Bio::Tools::Run::Glimmer is not present
> > t/Glimmer2.t .................. ok
> > t/Glimmer3.t .................. 1/111 # Required executable for
> > Bio::Tools::Run::Glimmer is not present
> > t/Glimmer3.t .................. ok
> > t/Gumby.t ..................... 1/124 # Required executable for
> > Bio::Tools::Run::Phylo::Gumby is not present
> > t/Gumby.t ..................... ok
> > t/Hmmer.t ..................... 1/27 # Required executable for
> > Bio::Tools::Run::Hmmer is not present
> > t/Hmmer.t ..................... ok
> > t/Hyphy.t ..................... 1/15 # Required executable for
> > Bio::Tools::Run::Phylo::Hyphy::SLAC is not present
> > t/Hyphy.t ..................... ok
> > t/Infernal.t .................. 1/43 # Required executable for
> > Bio::Tools::Run::Infernal is not present
> > t/Infernal.t .................. ok
> > t/Kalign.t .................... 1/8 # Required executable for
> > Bio::Tools::Run::Alignment::Kalign is not present
> > t/Kalign.t .................... ok
> > t/LVB.t ....................... 1/19 # Required executable for
> > Bio::Tools::Run::Phylo::LVB is not present
> > t/LVB.t ....................... ok
> > t/Lagan.t ..................... 2/12 # Required executable for
> > Bio::Tools::Run::Alignment::Lagan is not present
> > t/Lagan.t ..................... ok
> > t/MAFFT.t ..................... 1/17 # Required executable for
> > Bio::Tools::Run::Alignment::MAFFT is not present
> > t/MAFFT.t ..................... ok
> > t/MCS.t ....................... 1/24 # Required executable for
> > Bio::Tools::Run::MCS is not present
> > t/MCS.t ....................... ok
> > t/Maq.t ....................... 1/51 # Required executable for
> > Bio::Tools::Run::Maq is not present
> > t/Maq.t ....................... ok
> > t/Match.t ..................... 1/7 # Required executable for
> > Bio::Tools::Run::Match is not present
> > t/Match.t ..................... ok
> > t/Mdust.t ..................... 1/5 # Required executable for
> > Bio::Tools::Run::Mdust is not present
> > t/Mdust.t ..................... ok
> > t/Meme.t ...................... 1/25 # Required executable for
> > Bio::Tools::Run::Meme is not present
> > t/Meme.t ...................... ok
> > t/Minimo.t .................... 1/72 # Required executable for
> > Bio::Tools::Run::Minimo is not present
> > t/Minimo.t .................... ok
> > t/Molphy.t .................... 1/10 # Required executable for
> > Bio::Tools::Run::Phylo::Molphy::ProtML is not present
> > t/Molphy.t .................... ok
> > t/Muscle.t .................... 1/16 # Required executable for
> > Bio::Tools::Run::Alignment::Muscle is not present
> > t/Muscle.t .................... ok
> > t/Neighbor.t .................. 1/17 # Required executable for
> > Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
> > t/Neighbor.t .................. ok
> > t/Newbler.t ................... 1/98 # Required executable for
> > Bio::Tools::Run::Newbler is not present
> > t/Newbler.t ................... ok
> > t/Njtree.t .................... 1/6 # Required executable for
> > Bio::Tools::Run::Phylo::Njtree::Best is not present
> > t/Njtree.t .................... ok
> > t/PAML.t ...................... 1/28 # Required executable for
> > Bio::Tools::Run::Phylo::PAML::Codeml is not present
> > t/PAML.t ...................... ok
> > t/Pal2Nal.t ................... 1/9 # Required executable for
> > Bio::Tools::Run::Alignment::Pal2Nal is not present
> > t/Pal2Nal.t ................... ok
> > t/PhastCons.t ................. 1/181 # Required executable for
> > Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> > t/PhastCons.t ................. ok
> > t/Phrap.t ..................... 1/127 # Required executable for
> > Bio::Tools::Run::Phrap is not present
> > t/Phrap.t ..................... ok
> > t/Phyml.t ..................... 1/47 # Required executable for
> > Bio::Tools::Run::Phylo::Phyml is not present
> > t/Phyml.t ..................... ok
> > t/Primate.t ................... 1/8 # Required executable for
> > Bio::Tools::Run::Primate is not present
> > t/Primate.t ................... ok
> > t/Primer3.t ................... 1/9 # Required executable for
> > Bio::Tools::Run::Primer3 is not present
> > t/Primer3.t ................... ok
> > t/Prints.t .................... 1/7 # Required executable for
> > Bio::Tools::Run::Prints is not present
> > t/Prints.t .................... ok
> > t/Probalign.t ................. 1/13 # Required executable for
> > Bio::Tools::Run::Alignment::Probalign is not present
> > t/Probalign.t ................. ok
> > t/Probcons.t .................. 1/11 # Required executable for
> > Bio::Tools::Run::Alignment::Probcons is not present
> > t/Probcons.t .................. ok
> > t/Profile.t ................... 1/7 # Required executable for
> > Bio::Tools::Run::Profile is not present
> > t/Profile.t ................... ok
> > t/Promoterwise.t .............. 1/9 # Required executable for
> > Bio::Tools::Run::Promoterwise is not present
> > t/Promoterwise.t .............. ok
> > t/ProtDist.t .................. 1/14 # Required executable for
> > Bio::Tools::Run::Phylo::Phylip::ProtDist is not present
> > t/ProtDist.t .................. ok
> > t/ProtPars.t .................. 1/11 # Required executable for
> > Bio::Tools::Run::Phylo::Phylip::ProtPars is not present
> > t/ProtPars.t .................. ok
> > t/Pseudowise.t ................ 1/18 # Required executable for
> > Bio::Tools::Run::Pseudowise is not present
> > t/Pseudowise.t ................ ok
> > t/QuickTree.t ................. 1/13 # Required executable for
> > Bio::Tools::Run::Phylo::QuickTree is not present
> > t/QuickTree.t ................. ok
> > t/RepeatMasker.t .............. 1/12 RepeatMasker program not found as or
> > not executable.
> > # Required executable for Bio::Tools::Run::RepeatMasker is not present
> > t/RepeatMasker.t .............. ok
> > t/SABlastPlus.t ............... 1/65 # Required executable for
> > Bio::Tools::Run::BlastPlus is not present
> > # Looks like you planned 65 tests but ran 63.
> > t/SABlastPlus.t ............... Dubious, test returned 255 (wstat 65280,
> > 0xff00)
> > Failed 2/65 subtests
> > (less 59 skipped subtests: 4 okay)
> > t/SLR.t ....................... 1/7 # Required executable for
> > Bio::Tools::Run::Phylo::SLR is not present
> > t/SLR.t ....................... ok
> > t/Samtools.t .................. ok
> > t/Seg.t ....................... 1/8 # Required executable for
> > Bio::Tools::Run::Seg is not present
> > t/Seg.t ....................... ok
> > t/Semphy.t .................... 1/19 # Required executable for
> > Bio::Tools::Run::Phylo::Semphy is not present
> > t/Semphy.t .................... ok
> > t/SeqBoot.t ................... 1/9 # Required executable for
> > Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present
> > t/SeqBoot.t ................... ok
> > t/Signalp.t ................... 1/7 # Required executable for
> > Bio::Tools::Run::Signalp is not present
> > t/Signalp.t ................... ok
> > t/Sim4.t ...................... 1/23 # Required executable for
> > Bio::Tools::Run::Alignment::Sim4 is not present
> > t/Sim4.t ...................... ok
> > t/Simprot.t ................... 1/6 # Required executable for
> > Bio::Tools::Run::Simprot is not present
> > t/Simprot.t ................... ok
> > t/SoapEU-function.t ........... skipped: Valid email not provided; required
> > for tests
> > t/SoapEU-unit.t ............... # NOTE: No network access required for
> > these tests; all are local file-based.
> > t/SoapEU-unit.t ............... ok
> > t/StandAloneFasta.t ........... 1/15 # Required executable for
> > Bio::Tools::Run::Alignment::StandAloneFasta is not present
> > t/StandAloneFasta.t ........... ok
> > t/TCoffee.t ................... 1/27 # Required executable for
> > Bio::Tools::Run::Alignment::TCoffee is not present
> > t/TCoffee.t ................... ok
> > t/TigrAssembler.t ............. 1/88 # Required executable for
> > Bio::Tools::Run::TigrAssembler is not present
> > # Required executable for Bio::Tools::Run::TigrAssembler is not present
> > t/TigrAssembler.t ............. ok
> > t/Tmhmm.t ..................... 1/9 # Required executable for
> > Bio::Tools::Run::Tmhmm is not present
> > t/Tmhmm.t ..................... ok
> > t/TribeMCL.t .................. ok
> > t/Vista.t ..................... 1/7 # Vista.jar is not in your class
> > path:Exception in thread "main" java.lang.NoClassDefFoundError: Vista
> > t/Vista.t ..................... ok
> > t/gmap-run.t .................. 1/8 # Required executable for
> > Bio::Tools::Run::Alignment::Gmap is not present
> > t/gmap-run.t .................. ok
> > t/tRNAscanSE.t ................ 1/12 # Required executable for
> > Bio::Tools::Run::tRNAscanSE is not present
> > t/tRNAscanSE.t ................ ok
> >
> > Test Summary Report
> > -------------------
> > t/BEDTools.t (Wstat: 512 Tests: 45 Failed: 3)
> > Failed tests: 8, 26, 44
> > Non-zero exit status: 2
> > Parse errors: Bad plan. You planned 423 tests but ran 45.
> > t/Blat.t (Wstat: 65280 Tests: 20 Failed: 0)
> > Non-zero exit status: 255
> > Parse errors: Bad plan. You planned 33 tests but ran 20.
> > t/SABlastPlus.t (Wstat: 65280 Tests: 63 Failed: 0)
> > Non-zero exit status: 255
> > Parse errors: Bad plan. You planned 65 tests but ran 63.
> > Files=80, Tests=2642, 22 wallclock secs ( 0.44 usr 0.19 sys + 18.10 cusr
> > 1.84 csys = 20.57 CPU)
> > Result: FAIL
> > Failed 3/80 test programs. 3/2642 subtests failed.
> > CJFIELDS/BioPerl-Run-1.006900.tar.gz
> > ./Build test -- NOT OK
> > //hint// to see the cpan-testers results for installing this module, try:
> > reports CJFIELDS/BioPerl-Run-1.006900.tar.gz
> > Running Build install
> > make test had returned bad status, won't install without force
> > Failed during this command:
> > CJFIELDS/BioPerl-Run-1.006900.tar.gz : make_test NO
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
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