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Source: bioperl
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>,
Steffen Moeller <moeller@debian.org>,
Andreas Tille <tille@debian.org>,
Olivier Sallou <osallou@debian.org>
Section: science
Testsuite: autopkgtest-pkg-perl
Priority: optional
Build-Depends: debhelper (>= 10)
Build-Depends-Indep: perl,
# Unnecessary according to lintian, but building with sbuild shows the contrary.
libmodule-build-perl (>= 0.420000),
libio-string-perl,
libdata-stag-perl,
libtest-most-perl,
# Recommended in Build.PL (we want them to run the tests)
libace-perl,
libalgorithm-munkres-perl,
libarray-compare-perl,
libbio-asn1-entrezgene-perl,
libbio-samtools-perl,
libcgi-pm-perl | perl (<< 5.19),
libclone-perl,
libconvert-binary-c-perl,
libdbd-sqlite3-perl,
libdbd-mysql-perl,
libdbd-pg-perl,
libgd-perl,
libgraph-perl,
libgraphviz-perl,
libhtml-parser-perl,
libhtml-tableextract-perl,
liblist-moreutils-perl,
libpostscript-perl,
libset-scalar-perl,
libsoap-lite-perl,
libsort-naturally-perl,
libspreadsheet-parseexcel-perl,
libspreadsheet-writeexcel-perl,
libstorable-perl,
libsvg-perl,
libsvg-graph-perl,
libtest-pod-perl,
liburi-perl,
libxml-dom-xpath-perl,
libxml-parser-perl,
libxml-sax-perl,
libxml-sax-writer-perl,
libxml-twig-perl,
libxml-simple-perl,
libxml-writer-perl,
libxml-libxml-perl,
libwww-perl,
# Needed to avoid downloading DTDs during the tests and therefore fail when network is not available:
libxml-sax-expatxs-perl
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/git/debian-med/bioperl.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/bioperl.git
Homepage: http://www.bioperl.org/
Package: bioperl
Architecture: all
Depends: libbio-perl-perl (= ${source:Version}),
${misc:Depends},
${perl:Depends}
Recommends: bioperl-run,
# for the following see #650412
# most of `binary -help` outputs
perl-doc,
# some libraries already in libbio-perl-perl's Recommends:
# bp_biofetch_genbank_proxy
libhttp-message-perl,
libwww-perl,
libcache-cache-perl,
# bp_blast2tree
libbio-perl-run-perl,
# bp_bulk_load_gff
libdbi-perl,
# bp_chaos_plot
libgd-gd2-perl,
# bp_das_server
libapache-dbi-perl,
# bp_download_query_genbank
liburi-perl,
# bp_einfo
# liburi-perl
# libhttp-message-perl
libxml-simple-perl,
# bp_fast_load_gff
# libdbi-perl
# bp_fetch [not for local indexing]
# bp_flanks
# libhttp-message-perl
# bp_genbank2gff
# libhttp-message-perl
# libdbi-perl
# bp_genbank2gff3
libyaml-perl,
# bp_hivq
# libhttp-message-perl
# libxml-simple-perl
# bp_meta_gff
# libdbi-perl
# bp_netinstall
# bp_pairwise_kaks
# libbio-perl-run-perl
# bp_process_wormbase
libace-perl,
# bp_query_entrez_taxa
# bp_remote_blast
# bp_revtrans-motif
liblist-moreutils-perl,
# bp_taxid4species
libxml-twig-perl,
# bp_taxonomy2tree
libset-scalar-perl
Suggests: groff-base
Description: Perl tools for computational molecular biology
The Bioperl project is a coordinated effort to collect computational methods
routinely used in bioinformatics into a set of standard CPAN-style,
well-documented, and freely available Perl modules. It is well-accepted
throughout the community and used in many high-profile projects, e.g.,
Ensembl.
.
The recommended packages are needed to run some of the included
binaries, for a detailed explanation including the specific Perl
modules please see README.Debian.
.
The suggested package enhances the manual pages.
Package: libbio-perl-perl
Architecture: all
Section: perl
Depends: libio-string-perl,
libdata-stag-perl,
${misc:Depends},
${perl:Depends}
# Temporary workaround as bioperl-run has not been split
Recommends: bioperl-run | libbio-perl-run-perl,
# Recommended in Build.PL
libace-perl,
libalgorithm-munkres-perl,
libarray-compare-perl,
libbio-asn1-entrezgene-perl,
libclone-perl,
libconvert-binary-c-perl,
libdbd-sqlite3-perl,
libdbd-mysql-perl,
libdbd-pg-perl,
libgd-perl,
libgraph-perl,
libgraphviz-perl,
libhtml-parser-perl,
libhtml-tableextract-perl,
liblist-moreutils-perl,
libpostscript-perl,
libset-scalar-perl,
libsoap-lite-perl,
libsort-naturally-perl,
libspreadsheet-parseexcel-perl,
libspreadsheet-writeexcel-perl,
libstorable-perl,
libsvg-perl,
libsvg-graph-perl,
liburi-perl,
libxml-dom-xpath-perl,
libxml-parser-perl,
libxml-sax-perl,
libxml-sax-writer-perl,
libxml-simple-perl,
libxml-twig-perl,
libxml-writer-perl,
libxml-libxml-perl,
libwww-perl
Suggests: bioperl,
libxml-sax-expatxs-perl
# Needed to avoid downloading DTDs.
Breaks: grinder (<< 0.5.3-3~)
Replaces: grinder (<< 0.5.3-3~)
Description: BioPerl core perl modules
BioPerl is a toolkit of perl modules useful in building bioinformatics
solutions in Perl. It is built in an object-oriented manner so that many
modules depend on each other to achieve a task. The collection of modules in
libbio-perl-perl consist of the core of the functionality of bioperl.
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