Source: bioperl
Standards-Version: 4.7.4
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>,
 Étienne Mollier <emollier@debian.org>,
Section: science
Testsuite: autopkgtest-pkg-perl
Build-Depends:
 debhelper-compat (= 13),
# Unnecessary according to lintian, but building with sbuild shows the contrary.
 libmodule-build-perl,
Build-Depends-Indep:
 perl,
 rename,
 libio-string-perl,
 libdata-stag-perl,
 libtest-most-perl,
 libbio-alignio-stockholm-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,
 libclass-unload-perl,
 libcgi-pm-perl,
 libclone-perl,
 libconvert-binary-c-perl,
 libdbd-sqlite3-perl,
 libdbd-mysql-perl,
 libdbd-pg-perl,
 libgraph-perl,
 libgraphviz-perl,
 libhtml-parser-perl,
 libhtml-tableextract-perl,
 liblist-moreutils-perl,
 libpath-class-perl,
 libperlio-eol-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-differences-perl,
 libtest-exception-perl,
 libtest-memory-cycle-perl,
 libtest-pod-perl,
 libtest-weaken-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,
 libyaml-perl,
 libtest-requiresinternet-perl,
# Needed to avoid downloading DTDs during the tests and therefore fail when network is not available:
 libxml-sax-expatxs-perl,
Vcs-Browser: https://salsa.debian.org/med-team/bioperl
Vcs-Git: https://salsa.debian.org/med-team/bioperl.git
Homepage: http://www.bioperl.org/

Package: bioperl
Architecture: all
Depends:
 libbio-perl-perl (= ${source:Version}),
 ${misc:Depends},
 ${perl:Depends},
 libtest-most-perl,
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_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},
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,
 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.
 libbio-alignio-stockholm-perl,
# Temporary workaround as bioperl-run has not been split
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.
