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Dockerfile
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FROM ubuntu:18.04
LABEL org.label-schema.name="MoCaSeq"
LABEL org.label-schema.vcs-url="https://github.com/roland-rad-lab/MoCaSeq"
LABEL author="mathias.friedrich [@] tum.de"
LABEL maintainer="sebastian.lange [@] tum.de"
LABEL org.label-schema.url="https://www.imo.med.tum.de"
ENV TARGET_DIR /var/pipeline
ENV PACKAGE_DIR=/opt
ENV TEMP_DIR=/var/tmp
ENV HOME /var
ENV DEBIAN_FRONTEND noninteractive
ENV DEBCONF_NONINTERACTIVE_SEEN true
ENV LANGUAGE=en_US.UTF-8
ENV LANG=en_US.UTF-8
ENV LC_ALL=en_US.UTF-8
ENV PATH ${PATH}:${PACKAGE_DIR}/bin
ENV PERL5LIB ${PACKAGE_DIR}/vep-96:${PERL5LIB}
## Configure default locale, mostly to avoid problems with R (sorting etc.),
## see https://github.com/rocker-org/rocker/issues/19
## define a user to be available via runtime flag '--user docker'
## install essential system packages
RUN apt update \
&& apt install -y --no-install-recommends \
locales \
&& sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
&& dpkg-reconfigure --frontend=noninteractive locales \
&& update-locale LANG=en_US.UTF-8 \
&& mkdir -p ${PACKAGE_DIR}/bin \
&& apt upgrade -y \
&& apt install -y --no-install-recommends \
apt-utils \
ca-certificates \
dirmngr \
fonts-texgyre \
gpg-agent \
software-properties-common \
gosu \
&& apt -y --no-install-recommends upgrade \
&& apt install -y --no-install-recommends \
apt-transport-https \
alien \
ant \
autoconf \
automake \
bioperl \
build-essential \
bowtie \
bc \
cmake \
cpanminus \
curl \
default-jre \
g++ \
gdebi \
git \
git-all \
git-daemon-sysvinit \
gparted \
gnupg2 \
libbam-dev \
libbz2-dev \
libcairo2-dev \
libcurl3-dev \
libexpat1-dev \
libgd-dev \
libgsl0-dev \
libjemalloc-dev \
liblapacke-dev \
liblzma-dev \
libncurses5-dev \
libpng-dev \
libssl-dev \
libxml2-dev \
openssh-server \
pandoc \
parallel \
perl \
perl-base \
poppler-utils \
python \
python-dev \
rpm \
rsync \
sra-toolkit \
unzip \
wget \
xvfb \
zip \
zlib1g-dev \
&& add-apt-repository 'ppa:openjdk-r/ppa' \
&& add-apt-repository 'ppa:git-core/ppa' \
&& apt update \
&& apt install -y --no-install-recommends \
openjdk-8-jdk \
&& rm -rf /var/lib/apt/lists/* \
&& cd ${TEMP_DIR} \
&& curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash \
&& apt-get install git-lfs \
&& git lfs install \
&& wget -nv https://bootstrap.pypa.io/get-pip.py \
&& python2 get-pip.py \
&& rm get-pip.py \
&& pip2 install numpy \
&& pip2 install scipy \
matplotlib \
multiqc \
six \
deeptools \
pandas \
multiprocessing \
PyVCF \
ConfigParser \
Cheetah \
pysam \
fisher
RUN apt-get update \
&& apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
&& add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/' \
&& apt update \
&& apt install -y --no-install-recommends \
r-base=3.6.3-1bionic \
r-base-dev=3.6.3-1bionic \
&& rm -rf /var/lib/apt/lists/* \
&& R -e 'install.packages(pkgs=c("BiocManager"),dependencies=TRUE)' \
&& R -e 'BiocManager::install(pkgs=c("tidyverse","devEMF","GenomicRanges","optparse","zoo","ggplot2","CopywriteR","HMMcopy","DNAcopy","GenomeInfoDb","Biostrings","data.table","RColorBrewer","pheatmap","biomaRt","BSgenome.Mmusculus.UCSC.mm10","BSgenome.Hsapiens.UCSC.hg38","BSgenome.Hsapiens.UCSC.hg19","deconstructSigs","XML","LSD","randtests","svglite","dupRadar","SNPchip","TitanCNA","devtools","doMC","naturalsort","SomaticSignatures","SomaticCancerAlterations"),version="3.10",ask=FALSE,update=TRUE)'
RUN cd ${TEMP_DIR} \
&& curl -fsSL https://download.docker.com/linux/debian/gpg | apt-key add - \
&& add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable edge" \
; apt update \
&& apt install -y --no-install-recommends \
docker-ce docker-ce-cli containerd.io
RUN cd ${TEMP_DIR} \
# bwa-mem v0.7.17 (http://bio-bwa.sourceforge.net)
&& cd ${TEMP_DIR} \
&& wget -nv 'https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2' \
&& tar -xjvf bwa-0.7.17.tar.bz2 \
&& cd bwa-0.7.17 \
&& make \
&& cd ${TEMP_DIR} \
&& mv ./bwa-0.7.17 ${PACKAGE_DIR}/ \
&& ln -sf ${PACKAGE_DIR}/bwa-0.7.17/bwa ${PACKAGE_DIR}/bin/bwa \
&& rm -rf bwa-0.7.17.tar.bz2 \
# temporary files from bwa.kit are needed for human ref genome generation
&& cd ${TEMP_DIR} \
&& wget -nv 'https://sourceforge.net/projects/bio-bwa/files/bwakit/bwakit-0.7.15_x64-linux.tar.bz2' \
&& tar -xjf bwakit-0.7.15_x64-linux.tar.bz2 \
&& mv ./bwa.kit/resource-GRCh38 ${PACKAGE_DIR}/bwa-0.7.17/bwakit/ \
&& mv ./bwa.kit/resource-human-HLA ${PACKAGE_DIR}/bwa-0.7.17/bwakit/ \
&& mv bwa.kit ${PACKAGE_DIR}/bwakit-0.7.15 \
&& rm bwakit-0.7.15_x64-linux.tar.bz2 \
# htslib 1.10.2 and bcftools 1.10.2 and samtools 1.10
&& cd ${TEMP_DIR} \
&& git clone https://github.com/samtools/htslib.git \
&& git clone https://github.com/samtools/samtools.git \
&& git clone https://github.com/samtools/bcftools.git \
&& cd htslib \
&& git checkout '1.10.2' \
&& make \
&& make install \
&& cd ../bcftools \
&& git checkout '1.10.2' \
&& make \
&& make install \
&& cd ../samtools \
&& git checkout '1.10' \
&& make \
&& make install \
&& cd ${TEMP_DIR} \
&& rm -rf htslib bcftools samtools \
# bedtools v2.28.0 (https://github.com/arq5x/bedtools2)
&& cd ${TEMP_DIR} \
&& git clone https://github.com/arq5x/bedtools2.git \
&& cd bedtools2 \
&& git checkout 'v2.28.0' \
&& make \
&& make install \
&& cd ${TEMP_DIR} \
&& rm -rf bedtools2 \
# Delly2 v0.8.3 (https://github.com/dellytools/delly)
&& apt update \
&& apt install -y --no-install-recommends \
libboost-date-time-dev \
libboost-program-options-dev \
libboost-system-dev \
libboost-filesystem-dev \
libboost-iostreams-dev \
&& cd ${TEMP_DIR} \
&& wget https://github.com/dellytools/delly/releases/download/v0.8.3/delly_v0.8.3_linux_x86_64bit \
&& mkdir ${PACKAGE_DIR}/delly-0.8.3/ \
&& mv delly_v0.8.3_linux_x86_64bit ${PACKAGE_DIR}/delly-0.8.3/delly \
&& chmod a+x ${PACKAGE_DIR}/delly-0.8.3/delly \
&& ln -sf ${PACKAGE_DIR}/delly-0.8.3/delly ${PACKAGE_DIR}/bin/delly \
# Fasta-to-Fastq (https://github.com/ekg/fasta-to-fastq/)
&& cd ${TEMP_DIR} \
&& git clone https://github.com/ekg/fasta-to-fastq.git \
&& cp ./fasta-to-fastq/fasta_to_fastq.pl ${PACKAGE_DIR}/bin/ \
&& rm -rf fasta-to-fastq \
# GATK v3.8.1.0 (https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive\&version=3.8-1-0-gf15c1c3ef)
&& cd ${TEMP_DIR} \
&& wget -nv -O gatk-3.8.1.0.tar.bz2 'https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2' \
&& tar -xvjf gatk-3.8.1.0.tar.bz2 \
&& mv GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/ ${PACKAGE_DIR}/gatk-3.8.1.0 \
&& rm gatk-3.8.1.0.tar.bz2 \
# GATK v4.1.7.0 (https://software.broadinstitute.org/gatk/)
&& cd ${TEMP_DIR} \
&& wget -nv 'https://github.com/broadinstitute/gatk/releases/download/4.1.7.0/gatk-4.1.7.0.zip' \
&& unzip gatk-4.1.7.0.zip \
&& mkdir -p ${PACKAGE_DIR}/gatk-4.1.7.0 \
&& cp ./gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar ${PACKAGE_DIR}/gatk-4.1.7.0/ \
&& ln -sf ${PACKAGE_DIR}/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar ${PACKAGE_DIR}/gatk-4.1.7.0/gatk.jar \
&& rm -rf gatk-4.1.7.0.zip gatk-4.1.7.0 \
# GATK v4.1.4.1 (https://software.broadinstitute.org/gatk/)
&& cd ${TEMP_DIR} \
&& wget -nv 'https://github.com/broadinstitute/gatk/releases/download/4.1.4.1/gatk-4.1.4.1.zip' \
&& unzip gatk-4.1.4.1.zip \
&& mkdir -p ${PACKAGE_DIR}/gatk-4.1.4.1 \
&& cp ./gatk-4.1.4.1/gatk-package-4.1.4.1-local.jar ${PACKAGE_DIR}/gatk-4.1.4.1/ \
&& ln -sf ${PACKAGE_DIR}/gatk-4.1.4.1/gatk-package-4.1.4.1-local.jar ${PACKAGE_DIR}/gatk-4.1.4.1/gatk.jar \
&& rm -rf gatk-4.1.4.1.zip gatk-4.1.4.1 \
# GATK v4.1.3.0 (https://software.broadinstitute.org/gatk/)
&& cd ${TEMP_DIR} \
&& wget -nv 'https://github.com/broadinstitute/gatk/releases/download/4.1.3.0/gatk-4.1.3.0.zip' \
&& unzip gatk-4.1.3.0.zip \
&& mkdir -p ${PACKAGE_DIR}/gatk-4.1.3.0 \
&& cp ./gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar ${PACKAGE_DIR}/gatk-4.1.3.0/ \
&& ln -sf ${PACKAGE_DIR}/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar ${PACKAGE_DIR}/gatk-4.1.3.0/gatk.jar \
&& rm -rf gatk-4.1.3.0.zip gatk-4.1.3.0 \
# GATK v4.1.0.0 (https://software.broadinstitute.org/gatk/)
&& cd ${TEMP_DIR} \
&& wget -nv 'https://github.com/broadinstitute/gatk/releases/download/4.1.0.0/gatk-4.1.0.0.zip' \
&& unzip gatk-4.1.0.0.zip \
&& mkdir -p ${PACKAGE_DIR}/gatk-4.1.0.0 \
&& cp ./gatk-4.1.0.0/gatk-package-4.1.0.0-local.jar ${PACKAGE_DIR}/gatk-4.1.0.0/ \
&& ln -sf ${PACKAGE_DIR}/gatk-4.1.0.0/gatk-package-4.1.0.0-local.jar ${PACKAGE_DIR}/gatk-4.1.0.0/gatk.jar \
&& rm -rf gatk-4.1.0.0.zip gatk-4.1.0.0 \
# GATK requires Java 8 to be active
&& update-alternatives --set java /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java \
# HMMCopy Utils (https://github.com/shahcompbio/hmmcopy_utils/)
&& cd ${TEMP_DIR} \
&& git clone https://github.com/shahcompbio/hmmcopy_utils.git \
&& cd hmmcopy_utils \
&& cmake . \
&& make \
&& mkdir -p ${PACKAGE_DIR}/hmmcopy_utils \
&& cp -R ./bin ./util ${PACKAGE_DIR}/hmmcopy_utils/ \
&& cd ${TEMP_DIR} \
&& rm -rf hmmcopy_utils \
# fastQC v0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc)
&& cd ${TEMP_DIR} \
&& wget -nv 'www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.8.zip' \
&& unzip fastqc_v0.11.8.zip \
&& mv FastQC ${PACKAGE_DIR}/FastQC-0.11.8 \
&& chmod +x ${PACKAGE_DIR}/FastQC-0.11.8/fastqc \
&& ln -sf ${PACKAGE_DIR}/FastQC-0.11.8/fastqc ${PACKAGE_DIR}/bin/fastqc \
&& rm -rf fastqc_v0.11.8.zip \
# Picard v2.20.0 (https://broadinstitute.github.io/picard)
&& cd ${TEMP_DIR} \
&& wget -nv 'https://github.com/broadinstitute/picard/releases/download/2.20.0/picard.jar' \
&& mkdir -p ${PACKAGE_DIR}/picard-2.20.0 \
&& mv picard.jar ${PACKAGE_DIR}/picard-2.20.0 \
# sambamba v0.7.0 (https://broadinstitute.github.io/picard)
&& cd ${TEMP_DIR} \
&& wget -nv 'https://github.com/biod/sambamba/releases/download/v0.7.0/sambamba-0.7.0-linux-static.gz' \
&& gunzip sambamba-0.7.0-linux-static.gz \
&& mkdir -p ${PACKAGE_DIR}/sambamba-0.7.0 \
&& mv sambamba-0.7.0-linux-static ${PACKAGE_DIR}/sambamba-0.7.0/sambamba-0.7.0 \
&& chmod +x ${PACKAGE_DIR}/sambamba-0.7.0/sambamba-0.7.0 \
&& ln -sf ${PACKAGE_DIR}/sambamba-0.7.0/sambamba-0.7.0 ${PACKAGE_DIR}/bin/sambamba\
# SnpEff v4.3T (http://snpeff.sourceforge.net)
&& cd ${TEMP_DIR} \
&& wget -nv 'https://netix.dl.sourceforge.net/project/snpeff/snpEff_v4_3t_core.zip' \
&& unzip 'snpEff_v4_3t_core.zip' \
&& mv clinEff ${PACKAGE_DIR}/clinEff-4.3T \
&& mv snpEff ${PACKAGE_DIR}/snpEff-4.3T \
&& rm snpEff_v4_3t_core.zip \
&& wget -nv -O snpEff_v4_3_GRCh38.92.zip 'https://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_GRCh38.92.zip?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fsnpeff%2Ffiles%2Fdatabases%2Fv4_3%2FsnpEff_v4_3_GRCh38.92.zip%2Fdownload&ts=1556478741' \
&& unzip snpEff_v4_3_GRCh38.92.zip -d snpEff_v4_3_GRCh38.92 \
&& mkdir -p ${PACKAGE_DIR}/snpEff-4.3T/data \
&& mv snpEff_v4_3_GRCh38.92/data/GRCh38.92 ${PACKAGE_DIR}/snpEff-4.3T/data/GRCh38.92 \
&& echo 'GRCh38.92.genome : Homo_sapiens' >> ${PACKAGE_DIR}/snpEff-4.3T/snpEff.config \
&& echo 'GRCh38.92.reference : ftp://ftp.ensembl.org/pub/release-92/gtf/' >> ${PACKAGE_DIR}/snpEff-4.3T/snpEff.config \
&& rm snpEff_v4_3_GRCh38.92.zip \
&& rm -r snpEff_v4_3_GRCh38.92 \
&& wget -nv -O snpEff_v4_3_GRCm38.86.zip 'https://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_GRCm38.86.zip?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fsnpeff%2Ffiles%2Fdatabases%2Fv4_3%2FsnpEff_v4_3_GRCm38.86.zip%2Fdownload&ts=1557205135' \
&& unzip snpEff_v4_3_GRCm38.86.zip -d snpEff_v4_3_GRCm38.86 \
&& mv snpEff_v4_3_GRCm38.86/data/GRCm38.86 ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.86 \
# && echo 'GRCm38.86.genome : Homo_sapiens' >> ${PACKAGE_DIR}/snpEff-4.3T/snpEff.config \
# && echo 'GRCm38.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/' >> ${PACKAGE_DIR}/snpEff-4.3T/snpEff.config \
&& rm snpEff_v4_3_GRCm38.86.zip \
&& rm -r snpEff_v4_3_GRCm38.86 \
# Trimmomatic v0.39 (http://www.usadellab.org)
&& cd ${TEMP_DIR} \
&& wget -nv 'http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip' \
&& unzip Trimmomatic-0.39.zip \
&& mv Trimmomatic-0.39 ${PACKAGE_DIR}/trimmomatic-0.39 \
&& rm Trimmomatic-0.39.zip \
# msisensor v0.5 (https://github.com/ding-lab/msisensor, MSI testing)
&& cd ${TEMP_DIR} \
&& git clone 'https://github.com/ding-lab/msisensor.git' \
&& cd msisensor \
&& git checkout '0.5' \
&& make \
&& cp msisensor ${PACKAGE_DIR}/bin \
&& cd ${TEMP_DIR} \
&& rm -rf msisensor \
# Bam-matcher
&& cd ${TEMP_DIR} \
&& git clone 'https://bitbucket.org/sacgf/bam-matcher.git' \
&& mv ./bam-matcher ${PACKAGE_DIR}/ \
# Strelka 2.9.10 (https://github.com/Illumina/strelka)
&& cd ${TEMP_DIR} \
&& wget -nv 'https://github.com/Illumina/strelka/releases/download/v2.9.10/strelka-2.9.10.centos6_x86_64.tar.bz2' \
&& tar -xjf strelka-2.9.10.centos6_x86_64.tar.bz2 \
&& mv ./strelka-2.9.10.centos6_x86_64 ${PACKAGE_DIR}/strelka-2.9.10 \
&& rm strelka-2.9.10.centos6_x86_64.tar.bz2 \
# Manta 1.6.0 (https://github.com/Illumina/manta)
&& cd ${TEMP_DIR} \
&& wget -nv 'https://github.com/Illumina/manta/releases/download/v1.6.0/manta-1.6.0.centos6_x86_64.tar.bz2' \
&& tar -xjf manta-1.6.0.centos6_x86_64.tar.bz2 \
&& mv manta-1.6.0.centos6_x86_64 ${PACKAGE_DIR}/manta-1.6.0 \
&& rm manta-1.6.0.centos6_x86_64.tar.bz2 \
# VariantQC 1.07 (https://github.com/BimberLab/DISCVRSeq)
&& cd ${TEMP_DIR} \
&& wget -nv 'https://github.com/BimberLab/DISCVRSeq/releases/download/1.07/DISCVRSeq-1.07.jar' \
&& mkdir -p ${PACKAGE_DIR}/DISCVRSeq-1.07/ \
&& mv DISCVRSeq-1.07.jar ${PACKAGE_DIR}/DISCVRSeq-1.07/ \
# Vcftools 0.1.16 (https://github.com/vcftools/vcftools.git)
&& cd ${TEMP_DIR} \
&& git clone 'https://github.com/vcftools/vcftools.git' \
&& cd ./vcftools \
&& git checkout 'v0.1.16' \
&& ./autogen.sh \
&& ./configure \
&& make \
&& make install \
&& cd ${TEMP_DIR} \
&& rm -rf vcftools \
# GetBaseCounts v.1.2.2 (https://github.com/zengzheng123/GetBaseCountsMultiSample.git)
&& cd ${TEMP_DIR} \
&& git clone git://github.com/pezmaster31/bamtools.git \
&& cd bamtools/ \
&& mkdir -p build \
&& cd build/ \
&& cmake -DCMAKE_INSTALL_PREFIX=${TEMP_DIR}/bamtools .. \
&& make \
&& make install \
&& cd ${TEMP_DIR} \
&& git clone https://github.com/zengzheng123/GetBaseCountsMultiSample.git \
&& cd GetBaseCountsMultiSample \
&& git checkout 'v1.2.2' \
&& g++ -o3 -I${TEMP_DIR}/bamtools/include/bamtools -L${TEMP_DIR}/bamtools/lib/ GetBaseCountsMultiSample.cpp -lbamtools -lz -o GetBaseCountsMultiSample -fopenmp \
&& cp ./GetBaseCountsMultiSample ${PACKAGE_DIR}/bin/ \
&& cd ${TEMP_DIR} \
&& rm -rf bamtools GetBaseCountsMultiSample \
# Ensembl VEP 96.0 (https://github.com/Ensembl/ensembl-vep.git)
&& cd ${TEMP_DIR} \
&& git clone 'https://github.com/Ensembl/ensembl-vep.git' \
&& cd ensembl-vep \
&& git checkout 'release/96.0' \
&& cd ${TEMP_DIR} \
&& mv ensembl-vep ${PACKAGE_DIR}/vep-96 \
&& perl ${PACKAGE_DIR}/vep-96/INSTALL.pl --AUTO a --DESTDIR ${PACKAGE_DIR}/vep-96 --NO_UPDATE --NO_TEST --NO_HTSLIB \
# vcf2maf 1.6.17 (https://github.com/mskcc/vcf2maf/archive/v1.6.17.tar.gz)
&& cpanm --notest LWP::Simple Archive::Zip Archive::Extract HTTP::Tiny Test::Simple File::Copy::Recursive Perl::OSType Module::Metadata version TAP::Harness CGI Encode CPAN::Meta JSON DBD::SQLite Set::IntervalTree Archive::Tar Time::HiRes Module::Build Bio::Root::Version \
&& cd ${TEMP_DIR} \
&& wget -nv 'https://github.com/mskcc/vcf2maf/archive/v1.6.17.tar.gz' \
&& tar -xzf v1.6.17.tar.gz \
&& mv ./vcf2maf-1.6.17 ${PACKAGE_DIR} \
&& rm -rf v1.6.17.tar.gz
WORKDIR /var/pipeline/
RUN cd ${PACKAGE_DIR} \
&& git clone https://github.com/roland-rad-lab/MoCaSeq.git \
&& cd ${PACKAGE_DIR}/MoCaSeq/ \
&& chmod 775 entrypoint.sh \
&& chmod 775 MoCaSeq.sh \
&& chmod 775 repository/Meta_logstats.sh
ENTRYPOINT ["/opt/MoCaSeq/entrypoint.sh"]
CMD ["-h"]