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Commits on Apr 16, 2018
Commits on Apr 10, 2018
Commits on Apr 6, 2018
  1. Merge pull request #267 from matthdsm/master

    chapmanb committed Apr 6, 2018
    bumped vep version
Commits on Apr 4, 2018
  1. Improving hiding of boto imports for AWS work

    chapmanb committed Apr 4, 2018
    Avoids errors on GCP with boto. Fixes bcbio/bcbio-nextgen#2355
Commits on Apr 1, 2018
Commits on Mar 30, 2018
  1. Avoid boto import errors on GCE

    chapmanb committed Mar 30, 2018
    Avoid unneeded boto import to prevent incompatibilities with boto
    installed on GCE:
    
    https://stackoverflow.com/questions/40732313/gensim-installation-problems
    
    Fixes bcbio/bcbio-nextgen#2353
Commits on Mar 22, 2018
  1. Fixed prepare_tx_gff script, more 2bit indices

    chapmanb committed Mar 22, 2018
    Provides support for building transcripts and 2bits for
    mm10, rn6, canFam3
Commits on Mar 19, 2018
  1. hg38: update transcripts to ensembl release 91

    chapmanb committed Mar 19, 2018
    Improve script for generating transcripts, skipping indexing we now
    do on the fly instead of including in download.
Commits on Mar 17, 2018
Commits on Mar 9, 2018
Commits on Mar 6, 2018
  1. Revert back to snpEff 4.3 until next release

    chapmanb committed Mar 6, 2018
    Avoids issues with finding data inputs due to 4.3.1 sub version.
    Fixes bcbio/bcbio-nextgen#2314
Commits on Mar 2, 2018
  1. Improved fix for conda/libedit docker issues

    chapmanb committed Mar 2, 2018
    Only upgrade conda a single time prior to libedit removal. Otherwise
    run into similar upgrade issue with only conda and libedit removed.
  2. conda and java install issues with Docker builds

    chapmanb committed Mar 2, 2018
    - Ensure we have conda-forge synchronized conda (4.3) to avoid
      segfaults and errors due to libedit removal.
    - Move to latest snpEff to avoid double java/openjdk installs
Commits on Feb 24, 2018
  1. gnomad hg38: fix gencode chromosome remapping

    chapmanb committed Feb 24, 2018
    - Uses new chromosome mappings with gencode inputs
    - Delete lines without remappings
    - Reorder sed to apply more complex transformations first (chr1_moreinfo
      before chr1, and chr10 before chr1)
    Fixes #266
Commits on Feb 20, 2018
Commits on Feb 15, 2018
  1. Manifest: skip brew package info

    chapmanb committed Feb 15, 2018
    No longer used and can get potentially worrisome library errors
Commits on Feb 9, 2018
Commits on Feb 6, 2018
Commits on Feb 2, 2018
  1. RADAR: update with sorted, cleaned BEDs

    chapmanb committed Feb 2, 2018
    Fixes vcfanno problems with out of sort headers.
    Fixes bcbio/bcbio-nextgen#2249
Commits on Feb 1, 2018
  1. Avoid quiet install; remove nomkl

    chapmanb committed Feb 1, 2018
    - Avoid quiet install to prevent timeouts on Travis CI builds
    - Remove nomkl allowing nomkl decision outside of bcbio install
Commits on Jan 30, 2018
Commits on Jan 27, 2018
Commits on Jan 17, 2018
  1. Correctly check and copy hg19 cosmic file

    chapmanb committed Jan 17, 2018
    Fixes #265
Commits on Jan 16, 2018
  1. Merge pull request #264 from vladsaveliev/master

    chapmanb committed Jan 16, 2018
    Fix checking environments for conda 4.4
Commits on Jan 14, 2018
  1. COSMIC: update preparation scripts

    chapmanb committed Jan 14, 2018
    Fixes preparation scripts to handle downloads from sftp and copy
    into bcbio directory. Fixes #262
  2. Merge pull request #263 from matthdsm/cosmic_update

    chapmanb committed Jan 14, 2018
    made COSMIC filename more generic
Commits on Jan 10, 2018
  1. Provide S3 cache for mappability regions

    chapmanb committed Jan 10, 2018
    Fixes download issues to UCSC. Thanks to @ohofmann, @vladsaveliev
Commits on Jan 9, 2018
Commits on Jan 6, 2018
Commits on Dec 31, 2017
  1. conda: only create environments in packages

    chapmanb committed Dec 31, 2017
    Avoids extra environment creation, trying to avoid build issues
    for bcbio Docker containers on travis.
Commits on Dec 29, 2017
  1. gnomad: separate data target and install fixes

    chapmanb committed Dec 29, 2017
    Avoid issues with including as part of GEMINI
    (Fixes #2171, Fixes chapmanb/cloudbiolinux#254)
Commits on Dec 23, 2017