Source: bioperl-run Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: science Testsuite: autopkgtest-pkg-perl Priority: optional Build-Depends: debhelper (>= 11~) 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, ncoils, phylip, phyml, primer3, probcons, raxml, samtools, sim4, t-coffee, tigr-glimmer, wise, # Needed for the network tests: libwww-perl Standards-Version: 4.2.1 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: ${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, ncoils, 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, # 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-se, # non-free # 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: libbio-perl-perl (<< 1.7.1-1) Replaces: 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.