bcbio (1.1.5-1) unstable; urgency=medium

  * New upstream version.

  * Better clean after build
  * Tests still fail.

 -- Steffen Moeller <moeller@debian.org>  Fri, 24 May 2019 18:42:30 +0200

bcbio (1.1.4-2) UNRELEASED; urgency=medium

  * Team upload.
  * Recommends: umis

 -- Andreas Tille <tille@debian.org>  Thu, 16 May 2019 09:49:26 +0200

bcbio (1.1.4-1) unstable; urgency=medium

  * New upstream release.
    - Move to Python 3.6. A python2 environment in the install runs
      non python3 compatible programs. The codebase is still compatible
      with python 2.7 but will only get run and tested on python 3 for
      future releases.
    - RNA-seq: fix for race condition when creating the pizzly cache
    - RNA-seq: Add Salmon to multiqc report.
    - RNA-seq single-cell/DGE: Properly strip transcript versions from
      GENCODE GTFs.
    - RNA-seq: Faster and more flexible rRNA biotype lookup.
    - Move to R3.5.1, including updates to all CRAN and Bioconductor
      packages.
    - tumor-only germline prioritization: provide more useful germline
      filtering based on prioritization INFO tag (EPR) rather than filter
      field.
    - Install: do not require fabric for tool and data installs, making
      full codebase compatible with python 3.
    - variant: Filter out variants with missing ALT alleles output
      by GATK4.
    - GATK: enable specification of spark specific parameters with
      `gatk-spark` resources.
    - RNA-seq single-cell/DGE: added `demultiplexed` option. If set to
      True, treat the data as if it has already been demultiplexed into
      cells/wells.
    - Multiple orders of magnitude faster templating with thousands of
      input files.

  * Moved stringtie from suggested to recommended
  * Added dependency on xonsh for testing

 -- Steffen Moeller <moeller@debian.org>  Thu, 11 Apr 2019 12:56:58 +0200

bcbio (1.1.3-1) unstable; urgency=medium

  * Team upload.
  * New upstream release.
  * bcbio-doc: mark as "Multi-Arch: foreign"
  * debian/patches/python3.patch: removed, applied upstream
  * debian/control: bcbio-doc: section is "doc"
                               and add ${sphinxdoc:Built-Using}
                    python3-bcbio: section is "python"
  * debian/patches/spelling: fix a few spelling errors
  * debian/patches/include_tests

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sun, 10 Feb 2019 00:42:06 -0800

bcbio (1.1.2-3) unstable; urgency=medium

  * Demoted python3-seqcluster to become a recommendation
  * Packaged documentation, which also contributed a man page

 -- Steffen Moeller <moeller@debian.org>  Wed, 23 Jan 2019 15:04:57 +0100

bcbio (1.1.2-2) UNRELEASED; urgency=medium

  * Found Python3 incompatbility. Upstream has it already.

 -- Steffen Moeller <moeller@debian.org>  Mon, 21 Jan 2019 23:56:26 +0100

bcbio (1.1.2-1) UNRELEASED; urgency=medium

  * Initial release (Closes: #903386)

    TODO: Documentation not built

 -- Steffen Moeller <moeller@debian.org>  Thu, 17 Jan 2019 16:37:37 +0100
