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Commits on Mar 21, 2017
Commits on Mar 8, 2017
Commits on Mar 7, 2017
  1. Package sync with bcbio 1.0.2 release

    - Update svtyper to faster version now supported in release
    - Add nodejs for CWL support in Docker containers
    committed Mar 7, 2017
Commits on Mar 5, 2017
  1. Merge pull request #245 from matthdsm/master

    bumped snpEff version to 4.3i
    committed on GitHub Mar 5, 2017
  2. Merge pull request #243 from rchekaluk/rac/ubuntu-xenial

    Update OS packages for ubuntu xenial
    committed on GitHub Mar 5, 2017
Commits on Feb 28, 2017
Commits on Feb 27, 2017
  1. bcbio: add GRIDSS SV caller

    committed Feb 27, 2017
Commits on Feb 24, 2017
  1. bumped snpEff version to 4.3i

    matthdsm committed Feb 24, 2017
Commits on Feb 23, 2017
Commits on Feb 22, 2017
  1. Finalize GiaB 3.3.2 update: hg19, hg38

    Complements #244, adding update for hg19 and including additional
    genomes for hg38.
    committed Feb 22, 2017
  2. Merge pull request #244 from rjsicko/master

    Updated to giab 3.3.2
    committed on GitHub Feb 22, 2017
Commits on Feb 21, 2017
  1. Merge branch 'master' into master

    rjsicko committed on GitHub Feb 21, 2017
  2. Updated to giab 3.3.2

    rjsicko committed Feb 21, 2017
  3. SV deletion truth sets for NA24385

    Add deletion truth sets for NA24385 from both Genome in a Bottle and
    Crowd sourced gold-standards:
    
    chapmanb/bcbio-nextgen#963 (comment)
    committed Feb 21, 2017
Commits on Feb 8, 2017
Commits on Feb 6, 2017
  1. Install hg38 viral genomes for infection detection

    Includes hg38 viral genomes from TCGA prepared with bwa indexes
    committed Feb 6, 2017
Commits on Feb 4, 2017
  1. Merge pull request #242 from rchekaluk/rac/package-updates

    Update custom package URLs and versions
    committed on GitHub Feb 4, 2017
Commits on Feb 3, 2017
  1. Remove Millstone hack fecf7b5

    rchekaluk committed Feb 3, 2017
  2. Update velvet version

    rchekaluk committed Feb 3, 2017
  3. Update hydra url

    rchekaluk committed Feb 3, 2017
Commits on Feb 2, 2017
Commits on Jan 31, 2017
  1. Ensure RADAR uses temporary directory for sorting

    Avoid out of disk space errors when using global temporary directory.
    Thanks to Moiz Bootwalla
    https://groups.google.com/d/msg/biovalidation/I21KymcawwY/SedbQMazDQAJ
    committed Jan 31, 2017
Commits on Jan 19, 2017
Commits on Jan 18, 2017
  1. Fix mirdeep2 version

    lpantano committed Jan 18, 2017
Commits on Jan 17, 2017
  1. Package pinning for bcbio 1.0.1 release

    - FreeBayes, update to supported 1.1.0 with much faster runtimes
    - svtyper, pin to older 0.0.4 version until 0.1.1 SV typing is
      benchmarked/validated
    committed Jan 17, 2017
Commits on Jan 15, 2017
  1. Handle new conda 4.3 JSON info output

    Correctly pull package directory names from new JSON output. #1739
    committed Jan 15, 2017