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Commits on Oct 17, 2016
  1. @Lenbok

    rtg-tools: update to 3.7.1, bugfixes and minor improvements

    Lenbok committed Oct 17, 2016
    0b2c156
Commits on Aug 29, 2016
  1. @Lenbok

    Convert from sha1sum to sha256. Fixes #32

    Lenbok committed Aug 29, 2016
    0db7423
Commits on Aug 25, 2016
  1. @Lenbok

    rtg-tools: update to new release, 3.7

    Lenbok committed Aug 25, 2016
    2de956c
Commits on Aug 16, 2016
  1. @tseemann

    Remove freebayes - now in homebrew/science

    tseemann committed Aug 16, 2016
    2787206
Commits on Aug 14, 2016

  1. Merge pull request #31 from heuermh/vep-issue-30 

    vep: replace sha1 checksums with sha256, fix some brew audit warnings
    committed on GitHub Aug 14, 2016
    a954709
Commits on Aug 13, 2016
  1. @heuermh

    vep: replace sha1 checksums with sha256, fix some brew audit warnings

    heuermh committed Aug 13, 2016
    a83faa9
Commits on May 1, 2016

  1. Details on latest status; update moved recipes 

    - Document current status of homebrew-cbl #28
- Remove discovar, which moved to homebrew-science. Fixes #27
- Match sailfish-cbl class name. Fixes #26
    committed May 1, 2016
    74d0674
Commits on Mar 13, 2016
  1. @Lenbok

    rtg-tools: update to 3.6.2, bugfixes and minor improvements

    Lenbok committed Mar 13, 2016
    414d74a
Commits on Jan 28, 2016
  1. @Lenbok

    rtg-tools: update to 3.6.1, bugfixes and minor improvements

    Lenbok committed Jan 28, 2016
    ba14988
Commits on Dec 7, 2015
  1. @Lenbok

    rtg-tools: update to 3.6, with vcfeval/rocplot improvements

    Lenbok committed Dec 7, 2015
    883540c
Commits on Nov 20, 2015
  1. @mjafin

    Version bumped properly...

    mjafin committed Nov 20, 2015
    07a2843
  2. @mjafin

    Update VarDict java to 1.4.2 

    Fixes bug that introduced `nu` instead of nucleotides in certain insertions
    mjafin committed Nov 20, 2015
    e030828
Commits on Nov 9, 2015
  1. @lpantano

    Fix sha1 for miraligner.

    lpantano committed Nov 9, 2015
    24d74ca
  2. @lpantano

    Update miraligner for srnaseq.

    lpantano committed Nov 9, 2015
    712f7b9
Commits on Oct 27, 2015
  1. @lpantano

    Update seqbuster for srnaseq pipeline.

    lpantano committed Oct 27, 2015
    54f4937
Commits on Oct 16, 2015
  1. @Lenbok

    rtg-tools: Update to point release 3.5.2, with rocplot improvements,… 

    … bugfixes.
    Lenbok committed Oct 16, 2015
    445482e
Commits on Oct 15, 2015

  1. bcbio-variation-recall: 0.1.4 with caller annotations 

    Adds support for annotating callers supporting an ensemble
call (chapmanb/bcbio-nextgen#1018)
    committed Oct 15, 2015
    2f7c503
Commits on Oct 9, 2015

  1. gatk-framework: move to 3.4-46 

    Avoid errors dealing with new gVCF output.
Fixes chapmanb/bcbio-nextgen#1057
    committed Oct 9, 2015
    0f6f986
Commits on Oct 6, 2015

  1. VarDict: update to latest var2vcf scripts 

    This changes the behavior of the -M flag, which now provides the
previous behavior (filtering of germline mutations) instead of removing
them. The default correspondingly switches to -M in bcbio.
    committed Oct 6, 2015
    9340539
Commits on Oct 2, 2015

  1. manta: update to 0.29.0 with hg38 support

    committed Oct 2, 2015
    8dbb44e
Commits on Sep 30, 2015
  1. @roryk

    Add bcbio.rnaseq formula.

    roryk committed Sep 30, 2015
    1cf0b79
Commits on Sep 24, 2015
  1. @roryk

    Update sambamba to 0.5.8. 

    This has some fixes to the depth calculations.
    roryk committed Sep 24, 2015
    2eec881
Commits on Sep 18, 2015

  1. SV updates: manta 0.28.0, wham 1.70-161

    committed Sep 18, 2015
    8546dbd
Commits on Sep 13, 2015
  1. @Lenbok

    Update for the new RTG Tools release

    Lenbok committed Sep 13, 2015
    bc8b51c
Commits on Sep 5, 2015
  1. @roryk

    Merge branch 'master' of https://github.com/chapmanb/homebrew-cbl

    roryk committed Sep 5, 2015
    d402c07
  2. @roryk

    Add cloudbiolinux version of Sailfish formula. 

    Upstream is being slow about merging, so use this for now.
    roryk committed Sep 5, 2015
    06b91c4
Commits on Sep 2, 2015

  1. AGE: pre-build without -static -O3 which cause it to hang on CentOS

    committed Sep 2, 2015
    4ef526d

  2. AGE: pre-built binary with MetaSV fixes

    committed Sep 2, 2015
    52e912a
Commits on Sep 1, 2015

  1. wham: include new inversion fixes

    committed Sep 1, 2015
    76e9b91

  2. scalpel: ensure usage of external bamtools 

    Replace additional hardcoded path to internal bamtools (fixes #989)
    committed Sep 1, 2015
    4d95160
Commits on Aug 31, 2015

  1. scalpel: fix handling of external bcftools 

    - Correctly link to external homebrew bcftools. Fixes chapmanb/bcbio-nextgen#989
- Use external samtools and bcftools to avoid building in formula.
    committed Aug 31, 2015
    ce602c7
Commits on Aug 27, 2015

  1. WHAM: 1.7.0-154 with VCF GL allele fix

    committed Aug 27, 2015
    204b97e
Commits on Aug 26, 2015

  1. WHAM: VCF support, Scalpel: global bamtools 

    - Avoid compiling and using internal bamtools in Scalpel, instead
  preferring a global version. Avoids issues with libbamtools loading
  of internal version. Fixes chapmanb/bcbio-nextgen-vm#108
- Update WHAM to latest version supporting REF filling in the output.
    committed Aug 26, 2015
    f1b35dd
  2. @guillermo-carrasco

    Merge pull request #24 from guillermo-carrasco/master 

    Formula to install pbgzip from samtools
    guillermo-carrasco committed Aug 26, 2015
    65107a1
  3. @guillermo-carrasco

    Get pbgzip from the new standalone repo

    guillermo-carrasco committed Aug 26, 2015
    da20caf