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Jul 15, 2015 @bradtaylor Added a dockerfile to picard
1 FROM broadinstitute/java-baseimage
2 MAINTAINER Broad Institute DSDE <dsde-engineering@broadinstitute.org>
3
Jul 17, 2015 @bradtaylor Changes to picard Dockerfile
4 # Install ant, git for building
5 RUN apt-get update && \
6 apt-get --no-install-recommends install -y --force-yes \
7 git \
8 ant && \
9 apt-get clean autoclean && \
10 apt-get autoremove -y
11
12 # Assumes Dockerfile lives in root of the git repo. Pull source files into container
13 COPY build.xml /usr/picard/build.xml
14 COPY src /usr/picard/src
15 COPY lib /usr/picard/lib
Jul 15, 2015 @bradtaylor Added a dockerfile to picard
16 WORKDIR /usr/picard
17
Jul 17, 2015 @bradtaylor Changes to picard Dockerfile
18 # Clone out htsjdk. First turn off git ssl verification
19 RUN git config --global http.sslVerify false && git clone https://github.com/samtools/htsjdk.git
20
21 # Build the distribution jar, clean up everything else
Jul 17, 2015 @bradtaylor Provided a helper script for passing JVM args to docker.
22 RUN ant clean all && \
23 mv dist/picard.jar picard.jar && \
24 mv src/scripts/picard/docker_helper.sh docker_helper.sh && \
25 ant clean && \
26 rm -rf htsjdk && \
27 rm -rf src && \
28 rm -rf lib && \
29 rm build.xml
Jul 17, 2015 @bradtaylor Changes to picard Dockerfile
30
Aug 26, 2015 @chrishah add new WORKDIR to docker container
31 RUN mkdir /usr/working
32 WORKDIR /usr/working
33
34 ENTRYPOINT ["/usr/picard/docker_helper.sh"]
Aug 27, 2015 @chrishah add CMD
35 CMD [""]