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Source: bioperl-run
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>,
Andreas Tille <tille@debian.org>
Section: science
Testsuite: autopkgtest-pkg-perl
Priority: optional
Build-Depends: debhelper (>= 10)
Build-Depends-Indep: perl,
libmodule-build-perl,
bioperl,
# Recommended in Build.PL:
libalgorithm-diff-perl,
libipc-run-perl,
libio-string-perl,
libxml-twig-perl,
# Not yet available: libfile-sort-perl
# Needed for the tests, but not documented Upstream
libtest-most-perl,
libarray-compare-perl,
libtree-dagnode-perl,
# Needed for the regression tests: all Recommends of bioperl-run except embassy, that needs interactive setup.
amap-align,
bedtools,
blast2,
bowtie,
bwa,
clustalw,
emboss,
exonerate,
hmmer,
hyphy-mpi,
infernal,
kalign,
maq,
mafft,
muscle,
phylip,
phyml,
primer3,
probcons,
raxml,
samtools,
sim4,
t-coffee,
tigr-glimmer,
wise,
# Needed for the network tests:
libwww-perl
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/bioperl-run/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/bioperl-run/trunk/
Homepage: http://search.cpan.org/dist/BioPerl-Run/
Package: bioperl-run
Architecture: all
Depends: ${misc:Depends},
${perl:Depends},
bioperl,
libbio-perl-run-perl (= ${source:Version})
Recommends: amap-align,
bedtools,
blast2,
bowtie,
bwa,
clustalw,
emboss,
exonerate,
hmmer,
hyphy-mpi,
infernal,
kalign,
maq,
mafft,
muscle,
phylip,
phyml,
primer3,
probalign,
probcons,
raxml,
samtools,
sim4,
t-coffee,
tigr-glimmer,
wise
# Non-Free.
Suggests: gmap,
paml
# 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,
# coils,
# condense,
# drawgram,
# drawtree,
# eponine,
# fasta, # non-free, inofficial package for BioLinux
# footprinter,
# genemark-hmm,
# genscan,
# gerp,
# glimmer2,
# lagan, # packaging work in progress
# lvb,
# match,
# mcs,
# mdust,
# meme, # non-free, packaging work in progress
# minimo,
# neighbor,
# newbler,
# njtree,
# pal2nal,
# phastcons,
# phrap,
# primate,
# prints,
# profile,
# promoterwise,
# protdist,
# protpars,
# pseudowise,
# quikctree,
# repeatmasker,
# sablastplus,
# seg,
# semphy,
# seqboot,
# signalp,
# simprot,
# slr,
# soapeu,
# tigr-assembler,
# tmhmm,
# tribe,
# trnascan,
# 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: ${misc:Depends},
${perl:Depends},
libbio-perl-perl (>= 1.7.1-1)
Recommends: libalgorithm-diff-perl,
libipc-run-perl,
libio-string-perl,
libxml-twig-perl,
libwww-perl
Breaks: bioperl-run (<< 1.6.9), libbio-perl-perl (<< 1.7.1-1)
Replaces: bioperl-run (<< 1.6.9), libbio-perl-perl (<< 1.7.1-1)
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.
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