+# Install Arvados SDK into bcbio-nextgen Docker image.
+#
+# To build bcbio-nextgen:
+#
+# $ git clone https://github.com/chapmanb/bcbio-nextgen.git
+# $ cd bcbio-nextgen
+# $ docker build
+# $ docker tag <image> bcbio-nextgen
+#
+
FROM bcbio-nextgen
MAINTAINER Peter Amstutz <peter.amstutz@curoverse.com>
USER root
-RUN apt-get remove -q -y ruby && \
+# Install Ruby 2.1.0
+RUN apt-get remove --quiet --assume-yes ruby && \
curl -L https://get.rvm.io | bash -s stable && \
/usr/local/rvm/bin/rvm install 2.1.0 && \
/bin/mkdir -p /usr/src/arvados
ADD generated/arvados.tar.gz /usr/src/arvados/
+ENV GEM_HOME /usr/local/rvm/gems/ruby-2.1.0
+ENV GEM_PATH /usr/local/rvm/gems/ruby-2.1.0:/usr/local/rvm/gems/ruby-2.1.0@global
+ENV PATH /usr/local/rvm/gems/ruby-2.1.0/bin:/usr/local/rvm/gems/ruby-2.1.0@global/bin:/usr/local/rvm/rubies/ruby-2.1.0/bin:/usr/local/rvm/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
# Install dependencies and set up system.
# The FUSE packages help ensure that we can install the Python SDK (arv-mount).
-RUN /usr/bin/apt-get update && \
- /usr/bin/apt-get install -q -y python-dev python-llfuse python-pip \
+RUN /usr/bin/apt-get update && \
+ /usr/bin/apt-get install --quiet --assume-yes python-dev python-llfuse python-pip \
libio-socket-ssl-perl libjson-perl liburi-perl libwww-perl \
fuse libattr1-dev libfuse-dev && \
/usr/sbin/adduser --disabled-password \
--gecos 'Crunch execution user' crunch && \
- /usr/bin/install -d -o crunch -g crunch -m 0700 /tmp/crunch-job && \
+ /usr/bin/install --directory --owner=crunch --group=crunch --mode=0700 /keep /tmp/crunch-src /tmp/crunch-job && \
/bin/ln -s /usr/src/arvados /usr/local/src/arvados
-ENV GEM_HOME /usr/local/rvm/gems/ruby-2.1.0
-ENV GEM_PATH /usr/local/rvm/gems/ruby-2.1.0:/usr/local/rvm/gems/ruby-2.1.0@global
-ENV PATH /usr/local/rvm/gems/ruby-2.1.0/bin:/usr/local/rvm/gems/ruby-2.1.0@global/bin:/usr/local/rvm/rubies/ruby-2.1.0/bin:/usr/local/rvm/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
-
# Install Arvados packages.
RUN gem update --system && \
find /usr/src/arvados/sdk -name '*.gem' -print0 | \