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Dockerfile enhancements #8

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Dockerfile enhancements #8

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78bb0c8
Dockerfile: don't install sdkman into root's home directory
0xaf1f Feb 12, 2018
a40e933
Dockerfile: set DEBIAN_FRONTEND to noninteractive
0xaf1f Feb 12, 2018
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12 changes: 7 additions & 5 deletions docker/Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,22 +1,24 @@
FROM ubuntu:14.04
MAINTAINER Simon Sadedin "[email protected]"
ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update;
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
RUN apt-get update && \
apt-get install -y software-properties-common python-software-properties && \
apt-get install -y curl wget && \
apt-get install -y apt-transport-https && apt-get update
RUN apt-get install -y libcurl4-openssl-dev && apt-get install -y libxml2-dev && apt-get install -y r-base
ENV SDKMAN_DIR="/usr/local/sdkman"
RUN curl -s "https://get.sdkman.io" | bash && \
sed -i -e 's/sdkman_auto_answer=false/sdkman_auto_answer=true/g' /root/.sdkman/etc/config && \
bash -c 'source "/root/.sdkman/bin/sdkman-init.sh"; sdk install java 7u141-zulu;'
sed -i -e 's/sdkman_auto_answer=false/sdkman_auto_answer=true/g' /usr/local/sdkman/etc/config && \
bash -c 'source "/usr/local/sdkman/bin/sdkman-init.sh"; sdk install java 7u141-zulu;'
RUN apt-get install -y git
RUN cd /usr/local && \
git clone https://github.com/ssadedin/ximmer.git && cd ximmer && ./bin/install -q && \
echo 'JAVA="/root/.sdkman/candidates/java/current/bin/java"' >> /usr/local/ximmer/eval/pipeline/config.groovy && \
echo 'java { executable="/root/.sdkman/candidates/java/current/bin/java" }' >> /usr/local/ximmer/eval/pipeline/bpipe.config && \
echo 'JAVA="/usr/local/sdkman/candidates/java/current/bin/java"' >> /usr/local/ximmer/eval/pipeline/config.groovy && \
echo 'java { executable="/usr/local/sdkman/candidates/java/current/bin/java" }' >> /usr/local/ximmer/eval/pipeline/bpipe.config && \
cd /usr/local/ximmer; mkdir cache && cd cache && wget 'http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/dgvMerged.txt.gz' && \
cd /usr/local/ximmer/cache && wget 'http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz'
ENV PATH="/usr/local/ximmer/bin:${PATH}"
ENV JAVA_HOME=/root/.sdkman/candidates/java/current/bin/java
ENV JAVA_HOME=/usr/local/sdkman/candidates/java/current/bin/java