Source: bcbio
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>
Section: contrib/science
Testsuite: autopkgtest-pkg-python
Priority: optional
Build-Depends: debhelper-compat (= 12),
               dh-python,
               python3-all,
               python3-setuptools,
               python3-gffutils,
               python3-mock,
               python3-pandas,
               python3-pybedtools,
               python3-pysam,
               python3-pyvcf,
               python3-toolz,
               python3-tornado,
               python3-yaml,
               python3-scipy,
               python3-psutil,
               python3-joblib,
# for testing
               atropos,
               bedtools,
               biobambam2,
               gffread,
               grabix,
               hisat2,
#               mosdepth, # missing
               perl,
               picard,
               python3-biopython,
               python3-cyvcf2,
               python3-geneimpacts,
               python3-logbook,
               python3-nose,
               python3-requests,
               python3-pytest,
               python3-pytest-mock,
               bcftools,
               rna-star,
               salmon,
               samblaster,
               samtools,
               seqtk,
               tabix,
               tophat,
               tophat-recondition,
               wham-align,
               xonsh,
# documentation
               python3-sphinx
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/bcbio
Vcs-Git: https://salsa.debian.org/med-team/bcbio.git
Homepage: https://github.com/bcbio/bcbio-nextgen
Rules-Requires-Root: no

Package: python3-bcbio
Architecture: all
Section: contrib/python
Depends: ${python3:Depends},
         ${misc:Depends},
         python3-biopython,
         python3-cyvcf2,
         python3-joblib,
         python3-logbook,
         python3-matplotlib,
         python3-psutil,
         python3-pysam,
         python3-requests,
         python3-scipy,
         python3-six,
         python3-tornado
Recommends:
         python3-arrow,
         python3-geneimpacts,
         python3-h5py,
         python3-pyvcf,
         python3-seqcluster,
         python3-statsmodels,
         python3-tabulate
Suggests:
         bcbio-doc,
         python3-bioblend,
         python3-msgpack
Description: library for analysing high-throughput sequencing data
 This package installs the Python 3 libraries of the bcbio-nextgen
 toolkit implementing best-practice pipelines for fully automated high
 throughput sequencing analysis.
 .
 A high-level configuration file specifies inputs and analysis parameters
 to drive a parallel pipeline that handles distributed execution,
 idempotent processing restarts and safe transactional steps.  The project
 contributes a shared community resource that handles the data processing
 component of sequencing analysis, providing researchers with more time
 to focus on the downstream biology.

Package: bcbio
Architecture: all
Depends: ${python3:Depends},
         ${misc:Depends},
         python3-bcbio
Recommends: bcftools,
            cnvkit,
            cufflinks,
            delly,
            fastqc,
            freebayes,
            grabix,
            libvcflib-tools,
            macs,
            pythonpy,
            rna-star,
            hisat2,
            sambamba,
            samblaster,
            samtools,
            salmon,
            stringtie,
            subread,
            tabix,
            umis,
            varscan,
            wget,
            wham-align
Suggests: toil,
          cwltool,
          kallisto,
          bcbio-doc,
# still missing lumpy-sv,
# still missing manta,
# non-free, install manually: novoalign,
          qualimap,
# for cancer heterogeneity analysis with BubbleTree
          libglu1-mesa,
# for low mem instead of rna-star
          tophat2,
# found in source code but not exactly sure about its importance
          tophat-recondition,
          r-other-wasabi
Description: toolkit for analysing high-throughput sequencing data
 This package installs the command line tools of the bcbio-nextgen
 toolkit implementing best-practice pipelines for fully automated high
 throughput sequencing analysis.
 .
 A high-level configuration file specifies inputs and analysis parameters
 to drive a parallel pipeline that handles distributed execution,
 idempotent processing restarts and safe transactional steps.  The project
 contributes a shared community resource that handles the data processing
 component of sequencing analysis, providing researchers with more time
 to focus on the downstream biology.

Package: bcbio-doc
Architecture: all
Depends: ${sphinxdoc:Depends},${misc:Depends},
Suggests: bcbio|python3-bcbio
Built-Using: ${sphinxdoc:Built-Using}
Section: contrib/doc
Multi-Arch: foreign
Description: Documentation for RNAseq-workflows of bcbio(-nextgen)
 This package provides the documentation for all aspects of the
 workflows and technology of the bcbio-nextgen toolkit.
 .
 A high-level configuration file specifies inputs and analysis parameters
 to drive a parallel pipeline that handles distributed execution,
 idempotent processing restarts and safe transactional steps.  The project
 contributes a shared community resource that handles the data processing
 component of sequencing analysis, providing researchers with more time
 to focus on the downstream biology.
