USER root
-RUN apt-get update && \
- apt-get install -y -q openjdk-7-jre-headless && \
+RUN apt-get update -q
+RUN apt-get install -qy 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 && \
+ 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://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2 -o samtools-0.1.19.tar.bz2 && \
+ 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 && \