[ARVADOS] updated: 71035a6ed21e5acf4604b04bd7e046734efd650b

git at public.curoverse.com git at public.curoverse.com
Tue Jul 1 10:10:32 EDT 2014


Summary of changes:
 docker/build_tools/Makefile    |  6 ++++++
 docker/bwa-samtools/Dockerfile | 21 +++++++++++++++++++++
 2 files changed, 27 insertions(+)
 create mode 100644 docker/bwa-samtools/Dockerfile

       via  71035a6ed21e5acf4604b04bd7e046734efd650b (commit)
      from  f12986389693d4155847204210d9c84492ac6837 (commit)

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commit 71035a6ed21e5acf4604b04bd7e046734efd650b
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Jul 1 10:10:29 2014 -0400

    Add dockerfile to build arvados/jobs-bwa-samtools image. no issue #

diff --git a/docker/build_tools/Makefile b/docker/build_tools/Makefile
index 36f3654..81fa12f 100644
--- a/docker/build_tools/Makefile
+++ b/docker/build_tools/Makefile
@@ -26,6 +26,8 @@ BASE_DEPS = base/Dockerfile $(BASE_GENERATED)
 
 JOBS_DEPS = jobs/Dockerfile
 
+BWA_SAMTOOLS_DEPS = bwa-samtools/Dockerfile
+
 API_DEPS = api/Dockerfile $(API_GENERATED)
 
 DOC_DEPS = doc/Dockerfile doc/apache2_vhost
@@ -130,6 +132,10 @@ 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
+
 workbench-image: passenger-image $(BUILD) $(WORKBENCH_DEPS)
 	mkdir -p workbench/generated
 	tar -czf workbench/generated/workbench.tar.gz -C build/apps workbench
diff --git a/docker/bwa-samtools/Dockerfile b/docker/bwa-samtools/Dockerfile
new file mode 100644
index 0000000..cf19ee9
--- /dev/null
+++ b/docker/bwa-samtools/Dockerfile
@@ -0,0 +1,21 @@
+FROM arvados/jobs
+MAINTAINER Peter Amstutz <peter.amstutz at curoverse.com>
+
+USER root
+
+RUN 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 && \
+    make && \
+    (find . -executable -type f -print0 | xargs -0 -I {} mv {} /usr/local/bin) && \
+    rm -r /tmp/bwa-0.7.9a* && \
+    cd /tmp && \
+    curl --location http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2 -o samtools-0.1.19.tar.bz2 && \
+    tar xjf samtools-0.1.19.tar.bz2 && \
+    cd samtools-0.1.19 && \
+    make && \
+    (find . -executable -type f -print0 | xargs -0 -I {} mv {} /usr/local/bin) && \
+    rm -r /tmp/samtools-0.1.19*
+
+USER crunch
\ No newline at end of file

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