Source: gubbins
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>,
           Étienne Mollier <emollier@debian.org>
Section: science
Build-Depends: debhelper-compat (= 13),
               dh-sequence-python3,
               autoconf-archive,
               pkgconf,
               fasttree,
               iqtree,
               raxml,
               python3-setuptools,
               zlib1g-dev,
               check,
               python3,
               python3-biopython,
               python3-dendropy,
               python3-reportlab,
               tox <!nocheck>,
               python3-scipy <!nocheck>,
               python3-multiprocess <!nocheck>,
               python3-wheel <!nocheck>
Standards-Version: 4.7.3
Vcs-Browser: https://salsa.debian.org/med-team/gubbins
Vcs-Git: https://salsa.debian.org/med-team/gubbins.git
Homepage: https://nickjcroucher.github.io/gubbins/

Package: gubbins
Architecture: any
Depends: ${shlibs:Depends},
         ${misc:Depends},
         ${python3:Depends},
         python3,
         raxml
# FIXME: python3-numba is disabled until version 0.59 makes it back to testing.
# Delete also remove-numba-temporarily.patch when the time comes to bring back
# numba support in gubbins.
#        python3-numba
Recommends: iqtree,
            fasttree
Suggests: r-base-core
Description: phylogenetic analysis of genome sequences
 Gubbins supports rapid phylogenetic analysis of large samples of
 recombinant bacterial whole genome sequences.
 .
 Gubbins (Genealogies Unbiased By recomBinations In Nucleotide
 Sequences) is an algorithm that iteratively identifies loci containing
 elevated densities of base substitutions while concurrently constructing
 a phylogeny based on the putative point mutations outside of these
 regions. Simulations demonstrate the algorithm generates highly accurate
 reconstructions under realistic models of short-term bacterial
 evolution, and can be run in only a few hours on alignments of hundreds
 of bacterial genome sequences.