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.

Dockerfile

@@ -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 && \

docs/contents/configuration.rst

@@ -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

docs/contents/installation.rst

@@ -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/)