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Packages needed for the bioperl restructuring



On Sat, Sep 14, 2019 at 12:58 AM Andreas Tille <andreas@an3as.eu> wrote:

BTW, we should care for bioperl more seriosly to reflect the restructuring
of the upstream code.

Checking their changelog, here are some other modules that have their own packages since the Buster bioperl release 1.7.2:

as of bioperl version 1.7.5 2019-02-11:

Bio::Symbol::*

(no results in https://codesearch.debian.net/)

as of bioperl version 1.7.3 2019-01-30:

          Bio::DB::Ace
          Bio::DB::EMBL
Optional dependency for bioperl_1.7.5-1/bin/bp_fetch

          Bio::DB::GFF::Adaptor::*
          Bio::DB::GFF::Aggregator::*
          Bio::DB::GFF::Feature
          Bio::DB::GFF::RelSegment
          Bio::DB::SeqFeature::*
Used in  gbrowse, see https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=929506

          Bio::DB::GFF::Typename
appears to be optional requirement for libbio-graphics-perl whose tests have been failing since 2019-02-07 due to missing dependencies:
https://ci.debian.net/packages/libb/libbio-graphics-perl/unstable/amd64/
libbio-graphics-perl also needs Bio::DB::SeqFeature::*

          Bio::DB::GenBank
needed for an example script in libtfbs-perl: https://codesearch.debian.net/show?file=libtfbs-perl_0.7.1-2%2Fexamples%2Fscript1.pl&line=2
Its tests are still passing https://ci.debian.net/packages/libt/libtfbs-perl/
Also optional dependency for bioperl_1.7.5-1/bin/bp_fetch

          Bio::DB::GenPept
one example script in bioperl itself: https://codesearch.debian.net/show?file=bioperl_1.7.5-1%2Fexamples%2Ftk%2Fgsequence.pl&line=15
also optional dependency for bioperl_1.7.5-1/bin/bp_fetch

          Bio::DB::SwissProt
Optional dependency for bioperl itself: https://codesearch.debian.net/show?file=bioperl_1.7.5-1%2Ft%2FRemoteDB%2FSeqRead_fail.t&line=26

          Bio::LiveSeq::*
Optional dependency of bioperl itself https://codesearch.debian.net/search?q=Bio%3A%3ALiveSeq&literal=1

          Bio::SeqIO::entrezgene
Optional dependency of libbio-asn1-entrezgene-perl

          Bio::Taxonomy::*
Possible optional dependency of https://codesearch.debian.net/show?file=bioperl_1.7.5-1%2Flib%2FBio%2FTaxon.pm&line=139

          Bio::Cluster::*
          Bio::Tools::Run::RemoteBlast
Dependency of bioperl-run: https://codesearch.debian.net/show?file=bioperl-run_1.7.3-1%2Ft%2FTools%2FRun%2FRemoteBlast.t&line=16
bioperl-run is failing tests: https://ci.debian.net/data/autopkgtest/unstable/amd64/b/bioperl-run/2952351/log.gz
Can't locate File/Sort.pm
Can't locate Bio/DB/EUtilities.pm
Can't locate Bio/FeatureIO.pm
Can't locate Bio/Cluster/SequenceFamily.pm

          Bio::Tools::pSW
Optional dependency of bioperl https://codesearch.debian.net/show?file=bioperl_1.7.5-1%2Fexamples%2Falign%2Faligntutorial.pl&line=1

          Bio::Align::Graphics
          Bio::AlignIO::nexml
          Bio::AlignIO::stockholm
          Bio::Assembly::*
          Bio::ClusterI::*
          Bio::ClusterIO::*
          Bio::DB::BioFetch
          Bio::DB::CUTG
          Bio::DB::EntrezGene
          Bio::DB::_expression_::*
          Bio::DB::GFF
          Bio::DB::GFF::Featname
          Bio::DB::GFF::Homol
          Bio::DB::GFF::Segment
          Bio::DB::HIV::*
          Bio::DB::MeSH
          Bio::DB::NCBIHelper
          Bio::DB::Query::GenBank
          Bio::DB::Query::HIVQuery
          Bio::DB::RefSeq
          Bio::DB::SeqVersion::*
          Bio::DB::TFBS::*
          Bio::DB::Taxonomy::entrez
          Bio::DB::Taxonomy::sqlite
          Bio::DB::Universal
          Bio::Draw::Pictogram
          Bio::Factory::MapFactoryI
          Bio::Index::Hmmer
          Bio::Index::Stockholm
          Bio::Map::*
          Bio::MapIO::*
          Bio::MolEvol::CodonModel
          Bio::Nexml::Factory
          Bio::NexmlIO
          Bio::Phenotype::*
          Bio::PhyloNetwork::*
          Bio::PopGen::*
          Bio::Restriction::*
          Bio::Root::Build
          Bio::Search::HSP::HMMERHSP
          Bio::Search::HSP::HmmpfamHSP
          Bio::Search::Hit::HMMERHit
          Bio::Search::Hit::HmmpfamHit
          Bio::Search::Hit::hmmer3Hit
          Bio::Search::Result::HMMERResult
          Bio::Search::Result::HmmpfamResult
          Bio::Search::Result::hmmer3Result
          Bio::SearchDist
          Bio::SearchIO::hmmer2
          Bio::SearchIO::hmmer3
          Bio::SearchIO::hmmer_pull
          Bio::SeqEvolution::*
          Bio::SeqFeature::SiRNA::*
          Bio::SeqIO::abi
          Bio::SeqIO::agave
          Bio::SeqIO::alf
          Bio::SeqIO::chadoxml
          Bio::SeqIO::chaos
          Bio::SeqIO::chaosxml
          Bio::SeqIO::ctf
          Bio::SeqIO::excel
          Bio::SeqIO::exp
          Bio::SeqIO::flybase_chadoxml
          Bio::SeqIO::lasergene
          Bio::SeqIO::nexml
          Bio::SeqIO::pln
          Bio::SeqIO::strider
          Bio::SeqIO::ztr
          Bio::Structure::*
          Bio::Tools::AlignFactory
          Bio::Tools::Analysis::* (except SimpleAnalysisBase)
          Bio::Tools::Gel
          Bio::Tools::HMMER::*
          Bio::Tools::Hmmpfam
          Bio::Tools::Phylo::Gumby
          Bio::Tools::Protparam
          Bio::Tools::SiRNA::*
          Bio::Tools::dpAlign
          Bio::Tree::AlleleNode
          Bio::Tree::Draw::Cladogram
          Bio::TreeIO::nexml
          Bio::TreeIO::svggraph
          Bio::Variation::*

None of the above have any results in https://codesearch.debian.net/
 

Thanks for your work on this

      Andreas.

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http://fam-tille.de



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