[ARVADOS] created: 99a349f41ad1cc85865ceb1aa7485ceead70ff54

[git at public.curoverse.com]

        at  99a349f41ad1cc85865ceb1aa7485ceead70ff54 (commit)


commit 99a349f41ad1cc85865ceb1aa7485ceead70ff54
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Jul 1 17:05:18 2014 -0400

    Dockerfiles for java-bwa-samtools, bcbio-nextgen

diff --git a/docker/bcbio-nextgen/Dockerfile b/docker/bcbio-nextgen/Dockerfile
new file mode 100644
index 0000000..436aa9c
--- /dev/null
+++ b/docker/bcbio-nextgen/Dockerfile
@@ -0,0 +1,37 @@
+FROM bcbio-nextgen
+MAINTAINER Peter Amstutz <peter.amstutz at curoverse.com>
+
+USER root
+
+RUN apt-get remove -q -y 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/
+
+# 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 \
+      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 && \
+    /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 at global
+ENV PATH /usr/local/rvm/gems/ruby-2.1.0/bin:/usr/local/rvm/gems/ruby-2.1.0 at 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 | \
+      xargs -0rn 1 gem install && \
+    cd /usr/src/arvados/services/fuse && \
+    python setup.py install && \
+    cd /usr/src/arvados/sdk/python && \
+    python setup.py install
+
+USER crunch
diff --git a/docker/build_tools/Makefile b/docker/build_tools/Makefile
index 81fa12f..b279b4a 100644
--- a/docker/build_tools/Makefile
+++ b/docker/build_tools/Makefile
@@ -26,7 +26,7 @@ BASE_DEPS = base/Dockerfile $(BASE_GENERATED)
 
 JOBS_DEPS = jobs/Dockerfile
 
-BWA_SAMTOOLS_DEPS = bwa-samtools/Dockerfile
+JAVA_BWA_SAMTOOLS_DEPS = java-bwa-samtools/Dockerfile
 
 API_DEPS = api/Dockerfile $(API_GENERATED)
 
@@ -132,9 +132,15 @@ jobs-image: base-image $(BUILD) $(JOBS_DEPS)
 	$(DOCKER_BUILD) -t arvados/jobs jobs
 	date >jobs-image
 
-bwa-samtools-image: jobs-image $(BUILD) $(BWA_SAMTOOLS_DEPS)
-	$(DOCKER_BUILD) -t arvados/jobs-bwa-samtools bwa-samtools
-	date >bwa-samtools-image
+java-bwa-samtools-image: jobs-image $(BUILD) $(JAVA_BWA_SAMTOOLS_DEPS)
+	$(DOCKER_BUILD) -t arvados/jobs-java-bwa-samtools java-bwa-samtools
+	date >java-bwa-samtools-image
+
+bcbio-nextgen-image: $(BUILD) $(BASE_GENERATED) $(BCBIO_NEXTGEN_DEPS)
+	rm -rf bcbio-nextgen/generated
+	cp -r base/generated bcbio-nextgen
+	$(DOCKER_BUILD) -t arvados/bcbio-nextgen bcbio-nextgen
+	date >bcbio-nextgen-image
 
 workbench-image: passenger-image $(BUILD) $(WORKBENCH_DEPS)
 	mkdir -p workbench/generated
diff --git a/docker/bwa-samtools/Dockerfile b/docker/java-bwa-samtools/Dockerfile
similarity index 90%
rename from docker/bwa-samtools/Dockerfile
rename to docker/java-bwa-samtools/Dockerfile
index cf19ee9..e10f94f 100644
--- a/docker/bwa-samtools/Dockerfile
+++ b/docker/java-bwa-samtools/Dockerfile
@@ -3,7 +3,8 @@ MAINTAINER Peter Amstutz <peter.amstutz at curoverse.com>
 
 USER root
 
-RUN cd /tmp && \
+RUN apt-get install -y -q openjdk-7-jre-headless && \
+    cd /tmp && \
     curl --location http://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.9a.tar.bz2 -o bwa-0.7.9a.tar.bz2 && \
     tar xjf bwa-0.7.9a.tar.bz2 && \
     cd bwa-0.7.9a && \

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