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Verified Commit 1079c069 authored by Laurent Modolo's avatar Laurent Modolo
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hisat2: add samtools to docker

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src/docker_modules/hisat2/2.0.0/Dockerfile
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− 13
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FROM ubuntu:18.04 FROM samtools:1.7
MAINTAINER Nicolas Fontrodona MAINTAINER Nicolas Fontrodona
ENV HISAT2_VERSION=2.0.0 ENV HISAT2_VERSION=2.0.0
ENV PACKAGES unzip=6.0* \ ENV PACKAGES curl \
gcc=4:7.3.0* \ zip \
g++=4:7.3.0* \ g++ \
make=4.1* \ perl \
python \ python
curl=7.58.0* \
ca-certificates=20180409
RUN apt-get update && \ RUN apk update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \ apk add ${PACKAGES}
apt-get clean
RUN curl -k -L http://ccb.jhu.edu/software/hisat2/downloads/hisat2-${HISAT2_VERSION}-beta-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip && \ RUN curl -k -L http://ccb.jhu.edu/software/hisat2/downloads/hisat2-${HISAT2_VERSION}-beta-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip && \
unzip hisat2_linux-v${HISAT2_VERSION}.zip && \ unzip hisat2_linux-v${HISAT2_VERSION}.zip && \
...@@ -20,5 +17,4 @@ cd hisat2-${HISAT2_VERSION}-beta && \ ...@@ -20,5 +17,4 @@ cd hisat2-${HISAT2_VERSION}-beta && \
make && \ make && \
cp hisat2 /usr/bin && \ cp hisat2 /usr/bin && \
cp hisat2-* /usr/bin && \ cp hisat2-* /usr/bin && \
rm -Rf hisat2-${HISAT2_VERSION}-beta rm -Rf hisat2-${HISAT2_VERSION}-beta
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