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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>,
Étienne Mollier <emollier@debian.org>
Section: science
Testsuite: autopkgtest-pkg-perl
Priority: optional
Build-Depends: debhelper-compat (= 13), libmodule-build-perl
Build-Depends-Indep: perl,
bioperl (>= 1.7.4),
# Recommended in Build.PL:
libalgorithm-diff-perl,
libipc-run-perl,
libio-string-perl,
libxml-twig-perl,
libfile-sort-perl,
# Needed for the tests, but not documented Upstream
libtest-most-perl,
libarray-compare-perl,
libtree-dagnode-perl,
libbio-cluster-perl,
libbio-featureio-perl,
libconfig-any-perl,
libbio-tools-run-alignment-clustalw-perl [any-amd64],
libbio-eutilities-perl,
libbio-tools-run-remoteblast-perl,
# 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,
ncbi-blast+-legacy,
libbio-perl-perl,
clustalw [any-amd64],
emboss [any-amd64 arm64 mips64el ppc64el riscv64],
exonerate,
hmmer [any-amd64 any-i386 powerpc ppc64],
hyphy-pt | hyphy-mpi [any-amd64],
infernal [any-amd64 any-i386],
kalign,
mafft,
muscle,
ncoils,
# 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,
fasttree,
lagan,
pal2nal,
# probalign, # too old?
pftools [any-amd64],
# Needed for the network tests:
libwww-perl
Standards-Version: 4.7.0
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
Rules-Requires-Root: no
Package: bioperl-run
Architecture: all
Depends: ${misc:Depends},
${perl:Depends},
bioperl (>= 1.7.4),
libbio-perl-run-perl (= ${source:Version}),
libbio-featureio-perl,
libbio-cluster-perl,
libtest-requiresinternet-perl,
libbio-eutilities-perl,
libbio-tools-run-remoteblast-perl,
libsoap-lite-perl,
default-jdk-headless,
Recommends: amap-align,
ncbi-blast+-legacy,
bwa,
exonerate,
kalign,
maq,
mafft,
muscle,
ncoils,
phylip,
primer3,
probalign,
probcons,
raxml,
sim4,
t-coffee,
wise,
lagan,
pal2nal
Suggests: gmap,
fasta3,
trnascan-se,
bedtools,
bowtie,
clustalw,
emboss,
hmmer,
hyphy-pt | hyphy-mpi,
infernal,
libbio-tools-run-alignment-clustalw-perl,
pftools,
phyml,
samtools,
tigr-glimmer
# 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: ${misc:Depends},
${perl:Depends},
libbio-perl-perl,
libipc-run-perl,
libfile-sort-perl
Recommends: libalgorithm-diff-perl,
libio-string-perl,
libxml-twig-perl,
libwww-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.
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