Re: Bulk RFS Re: Packages needed for the bioperl restructuring
On Sun, Sep 15, 2019 at 01:31:35AM +0900, Michael Crusoe wrote:
> gbp clone git@salsa.debian.org:med-team/libbio-db-biofetch-perl.git
Please use lintian-brush 0.28 (from unstable/testing). It does a better
job with debian/upstream/metadata. I just "polished" with this version.
I also fixed the interpreter path inside the example.
> and 5 more below:
I'll do this later - real life things for today.
Thanks a lot for your preparation
Andreas.
> 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
>
>
> --
> Michael R. Crusoe
--
http://fam-tille.de
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