FROM arvados/jobs MAINTAINER Peter Amstutz USER root RUN apt-get update -qq RUN apt-get install -qqy openjdk-7-jre-headless && \ cd /tmp && \ curl --location http://cache.arvados.org/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://cache.arvados.org/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