Change log for bcbio package in Ubuntu

bcbio (1.2.9-2) unstable; urgency=medium

  * Team upload.
  * Fix watch file
  * Remove trailing whitespace in debian/changelog (routine-update)

 -- Andreas Tille <email address hidden>  Wed, 12 Oct 2022 09:38:21 +0200

Available diffs

• diff from 1.2.9-1 to 1.2.9-2 (572 bytes)

bcbio (1.2.9-1) unstable; urgency=medium

  * Team Upload
  
  [ Lance Lin ]
  * New upstream version - 1.2.9
  * Standards-Version: 4.6.1 
  * Copyright: updated years to cover 2022

 -- Lance Lin <email address hidden>  Wed, 17 Aug 2022 20:16:42 +0700

bcbio (1.2.5-1) unstable; urgency=medium

  * New upstream version.

 -- Steffen Moeller <email address hidden>  Tue, 26 Jan 2021 13:55:23 +0100

Available diffs

• diff from 1.2.4-2 to 1.2.5-1 (40.7 KiB)

bcbio (1.2.4-2) unstable; urgency=medium

  * Team upload.
  * Avoid calling Git - use Debian version to specify the code version
    Closes: #973804

 -- Andreas Tille <email address hidden>  Fri, 06 Nov 2020 11:16:33 +0100

Available diffs

• diff from 1.2.0-2 to 1.2.4-2 (295.0 KiB)
• diff from 1.2.4-1 to 1.2.4-2 (3.4 KiB)

bcbio (1.2.4-1) unstable; urgency=medium

  * New upstream version
  * debhelper-compat 13 (routine-update)

 -- Steffen Moeller <email address hidden>  Sat, 26 Sep 2020 00:56:30 +0200

bcbio (1.2.0-2) unstable; urgency=medium

  * Team upload.
  * Drop tophat from Build-Depends
    Closes: #953642
  * Add salsa-ci file (routine-update)

 -- Andreas Tille <email address hidden>  Wed, 11 Mar 2020 18:26:32 +0100

Available diffs

• diff from 1.2.0-1 to 1.2.0-2 (630 bytes)

bcbio (1.2.0-1) unstable; urgency=medium

  * New upstream version
  * debhelper-compat 12 (routine-update)
  * Remove trailing whitespace in debian/changelog (routine-update)
  * Remove trailing whitespace in debian/copyright (routine-update)
  * Remove trailing whitespace in debian/rules (routine-update)
  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
    Repository-Browse.
  * Adjusted path of bcbio-doc for doc-base

 -- Steffen Moeller <email address hidden>  Thu, 13 Feb 2020 18:30:04 +0100

Available diffs

• diff from 1.1.9-2 to 1.2.0-1 (22.0 KiB)

bcbio (1.1.9-2) unstable; urgency=medium

  * Team upload.
  * Drop tophat.

 -- Michael R. Crusoe <email address hidden>  Fri, 14 Feb 2020 17:23:23 +0100

Available diffs

• diff from 1.1.9-1 to 1.1.9-2 (1.7 KiB)

bcbio (1.1.9-1) unstable; urgency=medium

  * New upstream version.
  * Updated d/watch

 -- Steffen Moeller <email address hidden>  Wed, 11 Dec 2019 11:39:46 +0100

Available diffs

• diff from 1.1.8-1 to 1.1.9-1 (169.6 KiB)

bcbio (1.1.8-1) unstable; urgency=medium

  * New upstream version.

 -- Steffen Moeller <email address hidden>  Tue, 26 Nov 2019 14:05:42 +0100

Available diffs

• diff from 1.1.7-1 to 1.1.8-1 (16.4 KiB)

bcbio (1.1.7-1) unstable; urgency=medium

  * New upstream version.
 
  * Added directions to contrib to -doc and python- packages

 -- Steffen Moeller <email address hidden>  Sat, 19 Oct 2019 14:02:34 +0200

Available diffs

• diff from 1.1.5-1 to 1.1.7-1 (58.6 KiB)

bcbio (1.1.5-1) unstable; urgency=medium

  * New upstream version.

  * Better clean after build
  * Tests still fail.

 -- Steffen Moeller <email address hidden>  Fri, 24 May 2019 18:42:30 +0200

Available diffs

• diff from 1.1.4-1 to 1.1.5-1 (15.5 KiB)

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 <email address hidden>  Thu, 11 Apr 2019 12:56:58 +0200

Available diffs

• diff from 1.1.2-3 to 1.1.4-1 (111.3 KiB)

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 <email address hidden>  Wed, 23 Jan 2019 15:04:57 +0100