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Dockerfile
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FROM ubuntu:20.04 as builder
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get update \
&& apt-get --yes install \
build-essential \
openjdk-11-jdk-headless \
unzip \
wget \
python3 \
python3-pip \
zlib1g-dev \
&& rm -rf /var/lib/apt/lists/*
RUN pip3 install --ignore-installed \
--prefix /usr/local \
cwlref-runner \
html5lib
RUN cd /tmp \
&& wget https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2 \
&& echo "de1b4d4e745c0b7fc3e107b5155a51ac063011d33a5d82696331ecf4bed8d0fd *bwa-0.7.17.tar.bz2" | sha256sum --check \
&& tar xf bwa-0.7.17.tar.bz2 \
&& cd bwa-0.7.17 \
&& make -j$(nproc) \
&& mv bwa /usr/local/bin
RUN cd /tmp \
&& wget https://github.com/alexdobin/STAR/archive/refs/tags/2.7.10a.tar.gz \
&& echo "af0df8fdc0e7a539b3ec6665dce9ac55c33598dfbc74d24df9dae7a309b0426a *2.7.10a.tar.gz" | sha256sum --check \
&& tar xf 2.7.10a.tar.gz \
&& mv STAR-2.7.10a/bin/Linux_x86_64_static/STAR /usr/local/bin
# bz2 and lzma support is for CRAM files. curses is for `samtools tview`.
RUN cd /tmp \
&& wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 \
&& echo "083f688d7070082411c72c27372104ed472ed7a620591d06f928e653ebc23482 *samtools-1.9.tar.bz2" | sha256sum --check \
&& tar xf samtools-1.9.tar.bz2 \
&& cd samtools-1.9 \
&& ./configure \
--prefix /usr/local \
--disable-bz2 \
--disable-lzma \
--without-curses \
&& make -j$(nproc) \
&& make install
RUN cd /tmp \
&& wget https://github.com/biod/sambamba/releases/download/v0.7.0/sambamba-0.7.0-linux-static.gz \
&& echo "5a739ea53ef296639825831e110e359eab6ff421e108c7e3f4df0d67859e3024 *sambamba-0.7.0-linux-static.gz" | sha256sum --check \
&& gunzip sambamba-0.7.0-linux-static.gz \
&& mv sambamba-0.7.0-linux-static /usr/local/bin/sambamba \
&& chmod 0755 /usr/local/bin/sambamba
RUN cd /tmp \
&& wget https://services.gradle.org/distributions/gradle-5.4-bin.zip \
&& echo "c8c17574245ecee9ed7fe4f6b593b696d1692d1adbfef425bef9b333e3a0e8de *gradle-5.4-bin.zip" | sha256sum --check \
&& unzip gradle-5.4-bin.zip \
&& mv gradle-5.4 /opt/gradle
RUN mkdir -p /opt/picard/lib \
&& cd /opt/picard/lib \
&& wget -O picard-2.6.0.jar https://github.com/broadinstitute/picard/releases/download/2.6.0/picard.jar \
&& echo "671d9e86e6bf0c28ee007aea55d07e2456ae3a57016491b50aab0fd2fd0e493b *picard-2.6.0.jar" | sha256sum --check
ENV PATH /opt/gradle/bin:${PATH}
COPY bin /tmp/xenocp/bin
COPY src /tmp/xenocp/src
COPY dependencies /tmp/xenocp/dependencies
COPY gradle /tmp/xenocp/gradle
COPY gradlew /tmp/xenocp/gradlew
COPY build.gradle /tmp/xenocp/build.gradle
COPY settings.gradle /tmp/xenocp/settings.gradle
RUN cd /tmp/xenocp \
&& ./gradlew installDist \
&& cp -r build/install/xenocp /opt
FROM ubuntu:20.04
RUN apt-get update \
&& apt-get --yes install --no-install-recommends \
gawk \
nodejs \
openjdk-11-jre-headless \
python3 \
python3-distutils \
python-is-python3 \
file \
&& rm -rf /var/lib/apt/lists/*
COPY --chmod=755 --from=builder /usr/local/bin/cwl* /usr/local/bin/
COPY --chmod=755 --from=builder /usr/local/lib /usr/local/lib/
COPY --chmod=755 --from=builder /usr/local/bin/bwa /usr/local/bin/bwa
COPY --chmod=755 --from=builder /usr/local/bin/STAR /usr/local/bin/STAR
COPY --chmod=755 --from=builder /usr/local/bin/samtools /usr/local/bin/samtools
COPY --chmod=755 --from=builder /usr/local/bin/sambamba /usr/local/bin/sambamba
COPY --chmod=755 --from=builder /opt/picard /opt/picard
COPY --chmod=755 --from=builder /opt/xenocp /opt/xenocp
COPY --chmod=755 --from=builder /opt/xenocp/bin/* /usr/local/bin/
COPY --chmod=755 cwl /opt/xenocp/cwl