Source: bioperl-run
Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:
 Charles Plessy <plessy@debian.org>,
 Andreas Tille <tille@debian.org>,
 Étienne Mollier <emollier@debian.org>,
Section: science
Testsuite: autopkgtest-pkg-perl
Build-Depends:
 debhelper-compat (= 14),
 libmodule-build-perl,
Build-Depends-Indep:
# Needed for the regression tests: all Recommends of bioperl-run except embassy, that needs interactive setup.
 amap-align,
# While bedtools does install on i386 and other non-amd64 architectures, lack
# of python3-pybedtools is causing missing test data resulting in tests
# failures in bioperl-run, so the package is excluded on !amd64 for now.
 bedtools [any-amd64],
 bedtools-test,
 bioperl,
 clustalw [any-amd64],
 emboss [any-amd64 arm64 mips64el ppc64el riscv64],
 exonerate,
 fasttree,
 hmmer [any-amd64 any-i386 powerpc ppc64],
 hyphy-pt | hyphy-mpi [any-amd64],
 infernal [any-amd64 any-i386],
 kalign,
 lagan,
# Recommended in Build.PL:
 libalgorithm-diff-perl,
 libarray-compare-perl,
 libbio-cluster-perl,
 libbio-eutilities-perl,
 libbio-featureio-perl,
 libbio-perl-perl,
 libbio-tools-run-alignment-clustalw-perl [any-amd64],
 libbio-tools-run-remoteblast-perl,
 libconfig-any-perl,
 libfile-sort-perl,
 libio-string-perl,
 libipc-run-perl,
# Needed for the tests, but not documented Upstream
 libtest-most-perl,
 libtree-dagnode-perl,
# Needed for the network tests:
 libwww-perl,
 libxml-twig-perl,
 mafft,
 muscle,
 ncbi-blast+-legacy,
 ncoils,
 pal2nal,
 perl,
#                    probalign,  # too old?
 pftools [any-amd64],
#                    phylip, causes a test to fail
 phyml,
 primer3,
 probcons,
 python3-pybedtools [any-amd64],
 raxml,
 samtools [any-amd64],
 sim4,
 tigr-glimmer [any-amd64 arm64 mips64el ppc64el riscv64],
 wise,
Vcs-Browser: https://salsa.debian.org/med-team/bioperl-run
Vcs-Git: https://salsa.debian.org/med-team/bioperl-run.git
Homepage: https://metacpan.org/release/BioPerl-Run

Package: bioperl-run
Architecture: all
Depends:
 bioperl,
 default-jdk-headless,
 libbio-cluster-perl,
 libbio-eutilities-perl,
 libbio-featureio-perl,
 libbio-perl-run-perl (= ${source:Version}),
 libbio-tools-run-remoteblast-perl,
 libsoap-lite-perl,
 libtest-requiresinternet-perl,
 ${misc:Depends},
 ${perl:Depends},
Recommends:
 amap-align,
 bwa,
 exonerate,
 kalign,
 lagan,
 mafft,
 maq,
 muscle,
 ncbi-blast+-legacy,
 ncoils,
 pal2nal,
 phylip,
 primer3,
 probalign,
 probcons,
 raxml,
 sim4,
 t-coffee,
 wise,
Suggests:
 bedtools,
 bowtie,
 clustalw,
 emboss,
 fasta3,
 gmap,
 hmmer,
 hyphy-pt | hyphy-mpi,
 infernal,
 libbio-tools-run-alignment-clustalw-perl,
 pftools,
 phyml,
 samtools,
 tigr-glimmer,
 trnascan-se,
# gmap, fasta3, and trnascan-se is non-free
# Removed from Debian at all: molphy,
# Removed from Debian but might be reintroduced: ensembl,
# The following list of packages is not available in Debian:
# blat,
# cap3,
# condense,
# drawtree,
# eponine,
# footprinter,
# genemark-hmm,
# genscan,
# gerp, ( gerpcol )
# glimmer2,
# lvb,
# match,
# mcs,
# mdust,
# meme,		# non-free, packaging work in progress
# minimo,
# neighbor,
# newbler,
# njtree,
# phastcons,
# phrap,
# primate,
# prints,
# promoterwise,
# protdist,
# protpars,
# pseudowise,
# quicktree,
# repeatmasker,
# sablastplus,
# seg,
# semphy,
# seqboot,
# signalp,
# simprot,
# slr,
# soapeu,
# tigr-assembler,
# tmhmm,
# tribe,  + mcl, which is already packaged
# vista-align
Description: BioPerl wrappers: scripts
 Contains scripts from the BioPerl-Run package. This package will also install
 all wrappable applications packaged in Debian. The ones that are not Free are
 "Suggested" by this package.

Package: libbio-perl-run-perl
Architecture: all
Section: perl
Depends:
 libbio-perl-perl,
 libfile-sort-perl,
 libipc-run-perl,
 ${misc:Depends},
 ${perl:Depends},
Recommends:
 libalgorithm-diff-perl,
 libio-string-perl,
 libwww-perl,
 libxml-twig-perl,
Description: BioPerl wrappers: modules
 Contains modules that provide a Perl interface to various bioinformatics
 applications to allow them to be used with common BioPerl objects.
