/bcbio-nextgen

History for bcbio-nextgen/Dockerfile
Commits on Jul 18, 2017

  1. Skip bwakit in hg38 without HLA typing enabled 

    Testing for hg38 alignment slowdowns due to default bwakit
post-processing.
    committed Jul 18, 2017
    68c81d6

  2. docker: additional space cleanup to reduce image size

    committed Jul 18, 2017
    37e52e8
Commits on Jul 17, 2017

  1. docker: additional removal of large packages to reduce size

    committed Jul 17, 2017
    9ea0fc5

  2. docker: remove mkl and mysql to reduce image size

    committed Jul 17, 2017
    0870d7e
Commits on Jul 28, 2016

  1. Docker: minimize system dependencies in container 

    Simplify Docker container creation to avoid need for build system,
Java based system packages and X11 libraries. Attempt to reduce
overall container size now that we ship Java 8 as a conda package.
    committed Jul 28, 2016
    4955ce7
Commits on May 9, 2016

  1. Docker build: ensure tooldir specified 

    Allow initial install of tools when updating to development version.
    committed May 9, 2016
    5ca1d3b
Commits on Mar 29, 2016

  1. v0.9.7 release

    committed Mar 29, 2016
    c6f577d
Commits on Mar 25, 2016

  1. Reporting: do not run coverage summary by default 

    Coverage summary generation via Rscript and pandoc currently fails in
several cases, leading to scary looking error messages. We'll avoid
running for now and re-enable as part of general work to improve
coverage. Also remove documentation on installing pandoc since we
include that via conda.
    committed Mar 25, 2016
    2bf0501
Commits on Mar 9, 2016

  1. Do not remove qt: avoid conda recursive uninstall 

    Avoids removal of all packages that depend on qt (including bcbio)
as part of attempt to save space. Latest conda version recursively
uninstalls.
    committed Mar 9, 2016
    a2f564d
Commits on Feb 27, 2016

  1. Install: Do not check certificate to avoid Miniconda download issues

    committed Feb 27, 2016
    d17540b
Commits on Feb 23, 2016

  1. Add and document --datatarget option for data sets 

    Provide a single entry point, `--datatarget` for installing data
sub-sets or larger data files. This replaces partial support for this
in `--toolplus`. We now prefer GGD recipes for install of data and
data installs work by adjusting these annotations.

VEP is no longer installed by default to avoid long cache preparation
times for human samples. Enables installation of battenberg data
targets.
    committed Feb 23, 2016
    d88af1d
Commits on Feb 14, 2016

  1. Bump version used in Docker container

    committed Feb 14, 2016
    73b19a2
Commits on Jan 21, 2016

  1. Docker: cd out of removed directory

    committed Jan 21, 2016
    a8d164f

  2. docker: system packages supporting Arvados 

    Enables running using bcbio Docker images in Arvados without extra
additions. Thanks to @tomclegg.
    committed Jan 21, 2016
    a87be10
Commits on Jan 3, 2016

  1. CWL: work towards align split support + Docker 

    - Provide align_split as a string to allow passing to next steps
  in CWL.
- Update dockerfile to include up to date pandoc for
  QC generation.
    committed Jan 3, 2016
    17fad5a
Commits on Dec 14, 2015

  1. pip install: use global SSL, falling back to conda 

    More flexible use of SSL certificates with conda. We first try to
use the global one, only falling back to the conda installed SSL if
the global fails. This fixes #1156, where we need to use the global
SSL due to firewall restrictions.
    committed Dec 14, 2015
    c197123

  2. v0.9.5 Dockerfile build 

    Includes reduced library dependencies to match new conda-based
build.
    committed Dec 14, 2015
    8ab5938
Commits on Nov 4, 2015

  1. Create a single layer Dockerfile for hub.docker 

    Enable push/pull from hub.docker, and potential automated builds, by
creating the image as a single layer. Reduces total space for retrieval
and storage to similar to flattened gzip approach.
    committed Nov 4, 2015
    7a08c00
Commits on Aug 11, 2015

  1. Handle empty coverage BED files and simplify Dockerfile 

    - Skip running chanjo with empty BED files, fixing issues with unit tests.
- We no longer require site_perl setting for PERL5LIB in Dockerfile.
    committed Aug 11, 2015
    fd6cc0e
Commits on Aug 1, 2015

  1. Docker creation: fix download of pre-built genomes 

    - Fixes issue with missing genomes by avoiding bug in new code
  added for CWL support.
- Reduces size of Docker image by removing Homebrew git directory.
    committed Aug 1, 2015
    aabf6df
Commits on Feb 25, 2015

  1. Add bcbio anaconda installation to default PATH inside docker image. F… 

    …ixes #775
    committed Feb 25, 2015
    e036426
Commits on Jan 9, 2015
  1. @tetron

    Add bsdmainutils package to install 'hexdump' which is required to build 

    openssl package used by anaconda.
    tetron committed Jan 9, 2015
    2a5cfa8
Commits on Nov 16, 2014

  1. Move from plzip to pigz for parallel compression/decompression. Not m… 

    …uch practical space improvement with plzip
    committed Nov 16, 2014
    63d6508
Commits on Nov 15, 2014

  1. Fixes for on-demand genome downloads with no reference data. Update c… 

    …loud documentation to match no pre-build AMI
    committed Nov 15, 2014
    04dda10
Commits on Oct 11, 2014

  1. Default to a reduced number of split regions (200 instead of 2000) to… 

    … avoid controller memory issues with large sample sizes
    committed Oct 11, 2014
    6027e15
Commits on Sep 30, 2014

  1. Fix typo in Dockerfile (thanks to @brainstorm). Small cleanups in README

    committed Sep 30, 2014
    a20bf11
Commits on Jul 28, 2014

  1. Change installation defaults: no longer use sudo by default, and requ… 

    …ire explicit specification of genomes and aligners to install. Enables more minimal isolated installations
    committed Jul 28, 2014
    aa123a2
Commits on Jul 13, 2014

  1. Remove extra slash in continued line

    committed Jul 13, 2014
    8662bf2

  2. More work fixing paths and ld_library_path for docker #497

    committed Jul 13, 2014
    2
    51aaafa
Commits on Jul 10, 2014

  1. When building docker image, put environmental variable updates in /et… 

    …c/environment #497. Ensure bcbio symlinked into PATH when doing upgrades
    committed Jul 10, 2014
    71a2da8
Commits on Jul 5, 2014

  1. One more attempt to get isolation and sudo correct for phased installs

    committed Jul 5, 2014
    213fd27
Commits on Jul 4, 2014

  1. Correctly handle sudo during install to ensure system libraries insta… 

    …lled
    committed Jul 4, 2014
    a957bd4

  2. Provide full path to bcbio_nextgen for upgrades on module install

    committed Jul 4, 2014
    496aa3e

  3. Update dockerfile to be slightly more modular. Add documentation on s… 

    …etting ulimits on CentOS/RedHat
    committed Jul 4, 2014
    bb6bf12
Commits on Jun 14, 2014

  1. Generalize memoru scheduling to handle single core memory intensive p… 

    …rocesses alongside multi-CPU runs. Avoids overscheduling memory when programs do not run multicore and are using multiple cores for other programs
    committed Jun 14, 2014
    5a9d7c5