Bulk RFS Re: Packages needed for the bioperl restructuring

[Michael Crusoe <michael.crusoe@gmail.com>]

gbp clone git@salsa.debian.org:med-team/libbio-db-biofetch-perl.git

and 5 more below:

On Sat, Sep 14, 2019 at 7:25 PM Michael Crusoe <michael.crusoe@gmail.com> wrote:

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.

as of bioperl version 1.7.3 2019-01-30:

          Bio::DB::Ace

gbp clone git@salsa.debian.org:med-team/libbio-db-ace-perl.git

 

          Bio::DB::EMBL

gbp clone git@salsa.debian.org: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 git@salsa.debian.org: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 git@salsa.debian.org: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 git@salsa.debian.org: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

 

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Michael R. Crusoe