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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.
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1 parent 33a9ed5 commit 4955ce7d7e92795003b2e1495e27c75bd7ef7a41 @chapmanb committed Jul 28, 2016
Showing with 6 additions and 23 deletions.
  1. +4 −18 Dockerfile
  2. +1 −1 docs/contents/configuration.rst
  3. +1 −4 docs/contents/installation.rst
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@@ -1,29 +1,15 @@
FROM stackbrew/ubuntu:14.04
MAINTAINER Brad Chapman "https://github.com/chapmanb"
-# v0.9.7 -- https://github.com/chapmanb/bcbio-nextgen/commit/52cda3e
+# v1.0.0a -- https://github.com/chapmanb/bcbio-nextgen/commit/33a9ed5
# Setup a base system
RUN apt-get update && \
- apt-get install -y build-essential unzip wget git openjdk-7-jdk openjdk-7-jre && \
- apt-get install -y libglu1-mesa && \
- apt-get install -y curl pigz bsdmainutils && \
+ apt-get install -y curl wget git unzip tar gzip bzip2 xz-utils pigz && \
# Support inclusion in Arvados pipelines
apt-get install -y --no-install-recommends libcurl4-gnutls-dev mbuffer python2.7-dev python-virtualenv && \
-
-# Fake a fuse install; openjdk pulls this in
-# https://github.com/dotcloud/docker/issues/514
-# https://gist.github.com/henrik-muehe/6155333
- mkdir -p /tmp/fuse-hack && cd /tmp/fuse-hack && \
- apt-get install libfuse2 && \
- apt-get download fuse && \
- dpkg-deb -x fuse_* . && \
- dpkg-deb -e fuse_* && \
- rm fuse_*.deb && \
- echo -en '#!/bin/bash\nexit 0\n' > DEBIAN/postinst && \
- dpkg-deb -b . /fuse.deb && \
- dpkg -i /fuse.deb && \
- rm -rf /tmp/fuse-hack && \
+# Not added by default to save space
+# apt-get install -y libglu1-mesa && \
# bcbio-nextgen installation
mkdir -p /tmp/bcbio-nextgen-install && cd /tmp/bcbio-nextgen-install && \
@@ -540,7 +540,7 @@ Structural variant calling
==========================
- ``svcaller`` -- List of structural variant callers to use. [lumpy, manta,
- cnvkit, seq2c, battenberg]. LUMPY, Manta and DELLY require paired end reads.
+ cnvkit, seq2c, battenberg]. LUMPY and Manta require paired end reads.
- ``svprioritize`` -- Produce a tab separated summary file of structural
variants in regions of interest. This complements the full VCF files of
structural variant calls to highlight changes in known genes. This can be
@@ -43,10 +43,7 @@ The machine will need to have some basic requirements for installing and running
bcbio:
- Python 2.7, Python 3.x, or Python 2.6 plus the argparse dependency.
-- Basic system setup for unpacking files (tar, gunzip). This should be present
- on most non-minimal systems. On minimal Ubuntu machines, ``build-essential``
- provides this in one package.
-- unzip
+- Basic system setup for unpacking files: tar, gzip, unzip, bzip2, xz-utils.
- The git version control system (http://git-scm.com/)
- wget for file retrieval (https://www.gnu.org/software/wget/)

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