Source: bioperl-run Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: science Testsuite: autopkgtest-pkg-perl Priority: optional Build-Depends: debhelper-compat (= 13) Build-Depends-Indep: perl, libmodule-build-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, 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, bedtools, bedtools-test, ncbi-blast+-legacy, clustalw, emboss, exonerate, hmmer [any-amd64 any-i386 powerpc ppc64], hyphy-pt | hyphy-mpi, infernal [any-amd64 any-i386], kalign, mafft, muscle, ncoils, # phylip, causes a test to fail phyml, primer3, probcons, python3-pybedtools, raxml, samtools, sim4, tigr-glimmer, wise, fasttree, lagan, pal2nal, # probalign, # too old? pftools [any-amd64], # Needed for the network tests: libwww-perl Standards-Version: 4.5.1 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 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-tools-run-alignment-clustalw-perl, libbio-featureio-perl, libbio-cluster-perl, libtest-requiresinternet-perl, libbio-eutilities-perl, libbio-tools-run-remoteblast-perl, default-jdk-headless, hyphy-pt | hyphy-mpi Recommends: amap-align, bedtools, ncbi-blast+-legacy, bowtie, bwa, clustalw, emboss, exonerate, hmmer, infernal, kalign, maq, mafft, muscle, ncoils, phylip, phyml, primer3, probalign, probcons, raxml, samtools, sim4, t-coffee, tigr-glimmer, wise, lagan, pal2nal, pftools Suggests: gmap, fasta3, trnascan-se # 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 (>= 1.7.1-1), libipc-run-perl, libfile-sort-perl Recommends: libalgorithm-diff-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.