gbp clone [email protected]:med-team/libbio-db-biofetch-perl.git and 5 more below:
On Sat, Sep 14, 2019 at 7:25 PM Michael Crusoe <[email protected]> wrote: > > > On Sat, Sep 14, 2019 at 12:58 AM Andreas Tille <[email protected]> wrote: > > BTW, we should care for bioperl more seriosly to reflect the restructuring >> of the upstream code. >> > > as of bioperl version 1.7.3 2019-01-30: > > Bio::DB::Ace > gbp clone [email protected]:med-team/libbio-db-ace-perl.git > Bio::DB::EMBL > gbp clone [email protected]:med-team/libbio-db-embl-perl.git > 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 > gbp clone [email protected]:med-team/libbio-db-gff-perl.git > Bio::DB::SeqFeature::* > Used in gbrowse, see > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=929506 > gbp clone [email protected]:med-team/libbio-db-seqfeature-perl.git > 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 > Package is at https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl but it is blocked by https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl > > 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 > Waiting on https://github.com/bioperl/Bio-DB-SwissProt/issues/2 > Bio::LiveSeq::* > Optional dependency of bioperl itself > https://codesearch.debian.net/search?q=Bio%3A%3ALiveSeq&literal=1 > Waiting on https://github.com/bioperl/Bio-LiveSeq/issues/2 > Bio::SeqIO::entrezgene > Optional dependency of libbio-asn1-entrezgene-perl > Also waiting on https://github.com/bioperl/Bio-Variation/issues/2 > Bio::Taxonomy::* > Possible optional dependency of > https://codesearch.debian.net/show?file=bioperl_1.7.5-1%2Flib%2FBio%2FTaxon.pm&line=139 > Waiting on https://github.com/bioperl/Bio-Variation/issues/2 > > Bio::Cluster::* > Packaging at https://salsa.debian.org/med-team/libbio-cluster-perl but also waiting on Bio::Variation to be published to CPAN > Bio::Tools::Run::RemoteBlast > gbp clone [email protected]: med-team/libbio-tools-run-remoteblast-perl.git > 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 > No longer maintained as per https://github.com/bioperl/bioperl-ext#overall-notes -- Michael R. Crusoe
