9463: Setting up the checkpointer thread as a daemon so that it finishes when the...

[arvados.git] / docker / bcbio-nextgen / Dockerfile

diff --git a/docker/bcbio-nextgen/Dockerfile b/docker/bcbio-nextgen/Dockerfile
index 436aa9c1c4276bcb524f218822e6fff9582ec0a3..8f6e7745c5863f1a8ced4734d9905d11c2bf04a6 100644 (file)
--- a/docker/bcbio-nextgen/Dockerfile
+++ b/docker/bcbio-nextgen/Dockerfile
@@ -1,30 +1,40 @@
+# 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 | \