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Commits on Jun 29, 2016
Commits on Jun 21, 2016
  1. Merge pull request #222 from naumenko-sa/master

    	modified:   ggd-recipes/hg38/platinum-genome-NA12878.yaml
    committed on GitHub Jun 21, 2016
Commits on Jun 20, 2016
  1. @naumenko-sa
Commits on Jun 19, 2016
Commits on Jun 16, 2016
  1. Pins for bcftools and freebayes

    - Pin bcftools to 1.3.0 since 1.3.1 (samtools/bcftools#420) does not
      deal with Integer/Float issues from FreeBayes. GATK post-processing
      forces conversions to Integer for defined VCF attributes, causing
      failures. Prefer the 1.3.0 behavior of truncating to integers instead
      of failing.
    - Update FreeBayes to latest version with fixes for gVCF and GQ.
    committed Jun 16, 2016
Commits on Jun 11, 2016
  1. Avoid certificate errors for mm10: figshare -> s3

    figshare uses s3 as a backend, causing certificate errors for older wget
    with wildcare S3 certificates. Thanks to Jiantao Shi.
    committed Jun 11, 2016
  2. NA12878, NA24385, DREAM syn4 truth set updates

    - DREAM syn4 -- remove non 1-22,X,Y chromosomes from truth regions since
      not contained in set, avoiding false positives. Thanks to @scatreux
    - NA12878/NA24385 -- update to 3.2.2 truth set
    committed Jun 11, 2016
Commits on Jun 10, 2016
  1. Merge pull request #221 from naumenko-sa/master

    	modified:   ggd-recipes/hg19/platinum-genome-NA12878.yaml
    committed on GitHub Jun 10, 2016
  2. @naumenko-sa

    modified: ggd-recipes/hg19/platinum-genome-NA12878.yaml

    	modified:   ggd-recipes/hg38/platinum-genome-NA12878.yaml
    naumenko-sa committed Jun 10, 2016
Commits on Jun 9, 2016
Commits on Jun 7, 2016
Commits on Jun 6, 2016
Commits on Jun 3, 2016
  1. @lpantano
  2. @lpantano
  3. GGD recipe: hg38 dbSNP to stable repository

    Thanks to @ohofmann
    committed Jun 3, 2016
Commits on May 30, 2016
Commits on May 28, 2016
  1. GiaB truth sets: move to 3.2, add NA24385

    Update with new Genome in a Bottle v3.2 truth sets and add NA24385
    reference material calls.
    committed May 28, 2016
  2. hg38-noalt: update GGD for new NCBI url

    The alignment pipeline FTP repository at NCBI moved to a new location.
    Thanks to Jason Walker
    committed May 28, 2016
Commits on May 26, 2016
  1. @lpantano
Commits on May 24, 2016
  1. @lpantano
  2. @lpantano

    Adding ACMG56 genes for coverage QC step

    here we are! @ohofmann
    lpantano committed May 24, 2016
Commits on May 21, 2016
  1. Merge pull request #219 from geetduggal/patch-1

    Increase robustness of unpacking in secure containers
    committed May 21, 2016
Commits on May 20, 2016
  1. @geetduggal

    Increase robustness of unpacking in secure containers

    By adding the `--no-same-owner` option to the unpacking command, we avoid permission errors like what is below.  This can occur in more secure LXC or Docker setups where user ID namespaces that differ from the host.
    
    ```
    tar: GRCh37/rnaseq-2015-12-01/ref-transcripts.genePred: Cannot change ownership to uid 57074, gid 402011: Invalid argument
    tar: GRCh37/rnaseq-2015-12-01/tophat/GRCh37_transcriptome.1.bt2: Cannot change ownership to uid 57074, gid 402011: Invalid argument
    ...
    ```
    geetduggal committed May 20, 2016
Commits on May 14, 2016
  1. dbNSFP: only unpack if final file not present

    Avoids expensive operation on big dbNSFP files if user has pre-created
    inputs
    (chapmanb/bcbio-nextgen#1225 (comment))
    committed May 14, 2016
  2. biodata: use local tool path for hiSat2 indexing

    Avoids hisat2 index failures during bcbio install if PATH not yet
    set. Thanks to Jason Walker.
    committed May 14, 2016
Commits on May 12, 2016
  1. Remove RADAR from installed ggd-recipes

    RADAR download at Stanford is currently offline. We need to create a
    cached version for installation. Fixes chapmanb/bcbio-nextgen#1388
    committed May 12, 2016
Commits on May 10, 2016
  1. RTG index: explicitly set path to tooldir

    Use local free installed version of rtg for indexing, in case of other
    rtg versions installed on the system.
    committed May 10, 2016
Commits on May 8, 2016
  1. bcbio: fixed SNAP + new svtools

    - Pin SNAP to new fixed version for streaming, which appears
      to have a lower version number (since it's 'dev')
    - Update to latest svtools release with unified commandline
    committed May 8, 2016
Commits on May 4, 2016
  1. hg38 dbsnp to 147; new bcbio conda packages

    - Update hg38 dbsnp to version 147. Fixes chapmanb/bcbio-nextgen#1378
    - Add bamutil and gemini supporting tools to bcbio installation.
      chapmanb/bcbio-nextgen#1372
    committed May 4, 2016
Commits on Apr 28, 2016
  1. Doc: Add details about bcbio to README

    Provide a more friendly path for using CloudBioLinux through the
    bcbio installation. That is probably the default install most users
    want if they want to bootstrap a lot of tools. Fixes #218
    committed Apr 28, 2016
Commits on Apr 27, 2016
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