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FROM ubuntu:16.04
ENV bwa_version 0.7.17
ENV picard_version 2.17.11
ENV gatk4_version 4.0.6.0
ENV gatk3_version 3.8-1
ENV PATH "$PATH:/tmp/jre1.8.0_161/bin/"
ENV strelka2_version 2.9.2
ENV varscan_version 2.4.2
ENV snpeff_version 4_3t
ENV bedtools_version 2.17.0
ADD https://github.com/arq5x/bedtools/archive/v${bedtools_version}.tar.gz /tmp/
ADD http://downloads.sourceforge.net/project/bio-bwa/bwa-${bwa_version}.tar.bz2 /tmp/
ADD https://github.com/broadinstitute/picard/releases/download/${picard_version}/picard.jar /tmp/
ADD http://javadl.oracle.com/webapps/download/AutoDL?BundleId=230532_2f38c3b165be4555a1fa6e98c45e0808 /tmp/java.tar.gz
ADD https://github.com/broadinstitute/gatk/releases/download/${gatk4_version}/gatk-${gatk4_version}.zip /tmp/
ADD "https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=${gatk3_version}-0-gf15c1c3ef" /tmp/gatk3.bz2
ADD http://compgen.bio.unipd.it/downloads/java-7-oracle.tar.gz /tmp/java7.tar.gz
ADD https://github.com/Illumina/strelka/releases/download/v${strelka2_version}/strelka-${strelka2_version}.release_src.tar.bz2 /tmp/
ADD https://github.com/dkoboldt/varscan/releases/download/${varscan_version}/VarScan.v${varscan_version}.jar /tmp/
ADD https://raw.githubusercontent.com/alexcoppe/varscan_accessories/master/vs_format_converter.py /tmp/
ADD https://downloads.sourceforge.net/project/snpeff/snpEff_v${snpeff_version}_core.zip /tmp/
ADD https://raw.githubusercontent.com/alexcoppe/mutect-vcf-selector/master/mutect-vcf-selector.py /tmp/
ADD https://raw.githubusercontent.com/alexcoppe/iWhale/master/iwhale.py /usr/bin/iwhale
ADD https://raw.githubusercontent.com/alexcoppe/iWhale/master/SConstruct /tmp/
ADD https://raw.githubusercontent.com/alexcoppe/iWhale/master/configuration.py /tmp/
ADD https://raw.githubusercontent.com/alexcoppe/iWhale/master/Scons_variant_calling /tmp/
ADD https://raw.githubusercontent.com/alexcoppe/iWhale/master/update_GT_Strelka2.py /usr/local/bin/
RUN apt-get update \
&& chmod 755 /usr/local/bin/update_GT_Strelka2.py \
&& apt-get install -y apt-utils \
&& apt-get install -y python scons bzip2 make gcc zlib1g-dev unzip bedtools g++ samtools \
&& cd /tmp/ && tar xjvf bwa-${bwa_version}.tar.bz2 \
&& cd /tmp/bwa-${bwa_version} \
&& make \
&& mv /tmp/bwa-${bwa_version}/bwa /usr/bin \
&& cd /tmp/ && tar xvzf java.tar.gz \
&& tar xvzf java7.tar.gz \
&& tar xzvf v${bedtools_version}.tar.gz \
&& cd bedtools-${bedtools_version} \
&& make \
&& mv bin/* /usr/bin/ \
&& cd /tmp/ \
&& unzip gatk-${gatk4_version}.zip \
&& mv gatk-${gatk4_version} gatk4 \
&& tar xvjf gatk3.bz2 \
&& mv GenomeAnalysisTK-${gatk3_version}-0-gf15c1c3ef gatk3 \
&& tar -xjf strelka-${strelka2_version}.release_src.tar.bz2 \
&& mkdir build && cd build \
&& ../strelka-${strelka2_version}.release_src/configure --jobs=4 --prefix=/tmp/strelka \
&& make -j4 install \
&& cd /tmp/ && mv VarScan.v${varscan_version}.jar VarScan.jar \
&& cd /tmp/ \
&& unzip snpEff_v${snpeff_version}_core.zip \
&& rm -rf v${bedtools_version}.tar.gz bedtools-${bedtools_version} && rm /tmp/bwa-${bwa_version}.tar.bz2 && rm -rf /tmp/bwa-${bwa_version} && rm /tmp/java.tar.gz && rm /tmp/gatk-${gatk4_version}.zip && rm /tmp/gatk3.bz2 && rm snpEff_v${snpeff_version}_core.zip \
&& rm /tmp/java7.tar.gz && rm -rf strelka-${strelka2_version}.release_src.tar.bz2 strelka-${strelka2_version}.release_src
WORKDIR /working
ENTRYPOINT ["python","/usr/bin/iwhale","-s","/tmp"]