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FROM samtools:1.7
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MAINTAINER Nicolas Fontrodona

ENV HISAT2_VERSION=2.0.0
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ENV PACKAGES curl \
             zip \
             g++ \
             perl \
             python
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RUN apk update && \
    apk add ${PACKAGES}
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RUN curl -k -L http://ccb.jhu.edu/software/hisat2/downloads/hisat2-${HISAT2_VERSION}-beta-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip && \
unzip hisat2_linux-v${HISAT2_VERSION}.zip && \
cd hisat2-${HISAT2_VERSION}-beta && \
make && \
cp hisat2 /usr/bin && \
cp hisat2-* /usr/bin && \
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rm -Rf hisat2-${HISAT2_VERSION}-beta