/cloudbiolinux

History for cloudbiolinux/config/packages-homebrew.yaml
Commits on Aug 7, 2015

  1. Packages for metasv support + Biointerchange 

    - Add tools required for MetaSV: AGE, SPAdes and MetaSV conda package.
- Add pytabix requirements for mucor evaluation.
- Add Biointerchange brew formula (fixes #204)
    committed Aug 7, 2015
    890b73e
Commits on Feb 11, 2015

  1. Skip glia build to avoid issues with fsom library since not currently… 

    … used
    committed Feb 11, 2015
    1101b85
Commits on Jan 21, 2015

  1. Add lofreq brew package

    committed Jan 21, 2015
    afcfcd7
Commits on Dec 22, 2014
  1. @rchekaluk

    Yaha does not download at the moment.

    rchekaluk committed Dec 22, 2014
    293cf3a
Commits on Dec 11, 2014

  1. Update cufflinks to point to new binary locations. Use homebrew binar… 

    …y recipe instead of custom build. Thanks to Severine Catreux
    committed Dec 11, 2014
    4aaab86
Commits on Dec 9, 2014

  1. Skip libmaus builds, using pre-compiled biobambam distribution. Provi… 

    …des build speedup
    committed Dec 9, 2014
    a6af094
Commits on Nov 28, 2014

  1. Avoid brew conflicts with new build-only upstream version of sambamba… 

    … in homebrew-science
    committed Nov 28, 2014
    9377b56
Commits on Oct 24, 2014

  1. Add homebrew recipes for THetA2 and WHAM to default builds for bcbio … 

    …and cloudbiolinux
    committed Oct 24, 2014
    ac8ecf0
Commits on Sep 24, 2014

  1. samtools 1.x is now the default in homebrew, skip looking for --devel… 

    … versions and packages. Thanks to @mjafin
    committed Sep 24, 2014
    d18ce5c
Commits on Sep 19, 2014

  1. Add pindel and non-head seqtk to current bcbio packages

    committed Sep 19, 2014
    879deba
Commits on Sep 8, 2014

  1. Move to samtools 1.0, support brew version checking on devel versions

    committed Sep 8, 2014
    47c84ce
Commits on Aug 9, 2014

  1. Add delly structural variant caller with binary install. Enable passi… 

    …ng arguments to homebrew builds to enable
    committed Aug 9, 2014
    0306e1a
Commits on Jul 23, 2014

  1. Add vardict as default install target for bcbio. (chapmanb/bcbio-next… 

    …gen#514)
    committed Jul 23, 2014
    ebd4470
Commits on Jun 3, 2014

  1. Update to latest version of snpEff, GEMINI and VEP. Prefer brew insta… 

    …lls for snpEff and VEP, maintaining old snpEff for short-term back-compatibility
    committed Jun 3, 2014
    1183618
Commits on May 19, 2014

  1. Remove separate tabix install since tabix now included in bcftools as… 

    … of the latest release candidate
    committed May 19, 2014
    211a24a
Commits on Apr 4, 2014

  1. Add cramtools and rtg-tools support through brew installs. Remove old… 

    … custom cramtools install
    committed Apr 4, 2014
    8c73d29

  2. Include Staden io_lib with support for CRAM indexing and retrieval by… 

    … position
    committed Apr 4, 2014
    4509b98
Commits on Mar 15, 2014

  1. Move biobambam and libmaus build to brew packages instead of custom b… 

    …uilds. Clean up unused custom builds
    committed Mar 15, 2014
    d1bc63e
Commits on Feb 26, 2014

  1. Move to homebrew package for RNA-seq STAR aligner

    committed Feb 26, 2014
    5f52d4a
Commits on Feb 23, 2014

  1. Fix platypus brew target to avoid naming collision

    committed Feb 23, 2014
    30f8b18

  2. Move FreeBayes build to use brew recipe. Add Platypus caller

    committed Feb 23, 2014
    147bf6b
Commits on Dec 5, 2013

  1. Add homebrew versions of vcflib and glia packages, and make available… 

    … to bcbio-nextgen installer. chapmanb/bcbio-nextgen#204
    committed Dec 5, 2013
    d6e86ca
Commits on Dec 2, 2013

  1. Add fastx_toolkit as homebrew dependency instead of custom build. Inc… 

    …lude in bcbio-nextgen installation
    committed Dec 2, 2013
    abfc0ad
Commits on Nov 1, 2013

  1. Remove custom GNU parallel custom target, replacing with brew GNU par… 

    …allel build. Fixes chapmanb/bcbio-nextgen#160
    committed Nov 1, 2013
    b34d25f
Commits on Oct 31, 2013

  1. Re-enable additional brew-based builds with --env=inherit set thanks … 

    …to latest linuxbrew that allows use of external compiler environment Linuxbrew/legacy-linuxbrew#29
    committed Oct 31, 2013
    c5090aa
Commits on Oct 30, 2013

  1. Pin samtools to 0.1.19 version to avoid homebrew-science regression. F… 

    …ixes #125
    committed Oct 30, 2013
    85041eb
Commits on Oct 27, 2013

  1. Update sambamba to latest version with multicore support. Move to a h… 

    …omebrew recipe and remove older custom script.
    committed Oct 27, 2013
    383293b
Commits on Oct 23, 2013

  1. Remove homebrew build targets requiring more complicated builds until… 

    … we get a better handle on directing the gcc to use
    committed Oct 23, 2013
    cc0b3cd
Commits on Oct 22, 2013

  1. Enable homebrew/linuxbrew integration as part of default CloudBioLinu… 

    …x installation. Replace custom packages with homebrew equivalents. Update ngs_pipeline_minimal flavor for bcbio-nextgen builds
    committed Oct 22, 2013
    e057ad0
Commits on Sep 3, 2013

  1. Add support for MacOX Homebrew (and Linuxbrew port) package manager. … 

    …Provide preliminary framework for supporting MacOSX but needs testing and additional work
    committed Sep 3, 2013
    531c3ba