Skip to content


Subversion checkout URL

You can clone with
Download ZIP
branch: master
Commits on Jun 30, 2015
Commits on Jun 29, 2015
  1. Remove and rename additional Bio-Linux packages with support removed …

    …in the latest apt update. Fixes #201
Commits on Jun 24, 2015
Commits on Jun 21, 2015
  1. Initial support for hg19 in Battenberg, converting over input data fi…

    …les to use chr-prefixed contigs
Commits on Jun 19, 2015
Commits on Jun 17, 2015
Commits on Jun 12, 2015
Commits on Jun 11, 2015
Commits on Jun 8, 2015
  1. Support for changes to Linuxbrew: correctly detect if packages are li…

    …nked with descriptions. Avoid keeping curl around if installed, since Linuxbrew will use it over system curl and break
Commits on Jun 6, 2015
Commits on Jun 5, 2015
  1. Do not upgrade system when running ngs_pipeline_minimal to avoid bcbi…

    …o install being too intrusive on system. Fixes #193
  2. Additional Sanger Cancer tool requirements, including vcftools Perl i…

    …nstall. Simplify PERL5LIB requirements now that we don't use custom brew Perl install
Commits on Jun 3, 2015
  1. Additional requirements for Sanger::CGP tools and better cleanup of d…

    …ependencies we want to remove
  2. Generalize support for perl libraries and link with brew install of c…

    …panminus. Enables support for Sanger CGP tools, including Battenberg
Commits on May 30, 2015
Commits on May 22, 2015
Commits on May 21, 2015
Commits on May 20, 2015
  1. @brentp
  2. @brentp

    bump grabix version

    brentp authored
Commits on May 15, 2015
  1. bcbio: build targets for BubbleTree for heterogeneity analysis. Clean…

    … up installation to avoid re-installs of htslib and bwa
Commits on May 14, 2015
  1. @brentp

    grabix: bump version to 0.1.5

    brentp authored
Commits on May 13, 2015
  1. @roryk

    Less strict GTF cleaning.

    roryk authored
    Keep items with a 'gene_id' but no 'transcript_id'. When loading, guess
    if the file has 'gene' and 'transcript' items already, and if so, skip
    inferring them.
    Addresses concerns in daler/gffutils#48. Brings RNA-sew support for
    GRCh38 closer, addressing chapmanb/bcbio-nextgen#817. Some related
    discussion in chapmanb/bcbio-nextgen#849 as well.
Commits on May 11, 2015
Commits on May 9, 2015
  1. Handle pkg-config required input for cmake dependencies and unlink po…

    …tential conflicting packages used for builds after finished
Something went wrong with that request. Please try again.