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oncokb-annotator-3.4.0.def
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oncokb-annotator-3.4.0.def
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Bootstrap: docker
From: ubuntu:20.04
%labels
Application_name oncokb-annotator 3.4.0
Author Julia Wiggeshoff
Author_email [email protected]
Year 2024
%post
apt-get update
export DEBIAN_FRONTEND=noninteractive
apt-get install -y --no-install-recommends tzdata
ln -fs /usr/share/zoneinfo/Europe/Berlin /etc/localtime
dpkg-reconfigure --frontend noninteractive tzdata
apt-get install -y -f --no-install-recommends build-essential fakeroot \
bzip2 \
ca-certificates \
make \
gcc \
g++ \
cpanminus \
curl \
git \
libcurl4-openssl-dev \
libhts-dev \
libtabixpp-dev \
libtabixpp0 \
libmysqlclient-dev \
libpng-dev \
libbz2-dev \
liblzma-dev \
libncurses5-dev \
libncursesw5-dev \
locales \
openssl \
perl \
perl-base \
pandoc \
pkg-config \
python3 \
python3-dev \
python3-pip \
tabix \
unzip \
zlib1g && apt-get clean && rm -rf /var/lib/apt/lists/*
export LANG=C.UTF-8
export LC_ALL=C.UTF-8
cpanm -f Compress::Raw::Zlib IO::File Getopt::Long Pod::Usage DBI Bio::Root::Version \
File::Copy File::Path Text::Wrap File::Temp Archive::Zip DBD::mysql
mkdir -p /opt && cd /opt
git clone https://github.com/Ensembl/ensembl-vep.git
git clone https://github.com/oncokb/oncokb-annotator.git
git clone https://github.com/samtools/samtools.git
git clone https://github.com/samtools/htslib.git
git clone https://github.com/mskcc/vcf2maf.git
cd htslib && git checkout -b 57de9bc && git submodule update --init --recursive && make
cd ../samtools && git checkout -b 1f96fa8 && git submodule update --init --recursive && make
cd ../ensembl-vep && git checkout -b 1066f68 && git submodule update --init --recursive
perl INSTALL.pl --AUTO a
cd ../oncokb-annotator && git checkout -b 11d262d && git submodule update --init --recursive
echo "matplotlib==3.1.2" >> requirements/pip3.txt
pip install -r requirements/common.txt -r requirements/pip3.txt
cd ../vcf2maf && git checkout -b 754d68a
sed -i 's/STRAND_VEP/TRANSCRIPT_STRAND/g' vcf2maf.pl
cd ../
perl vcf2maf/vcf2maf.pl --help || exit 1
perl vcf2maf/maf2maf.pl --help || exit 1
python3 --version || exit 1
python3 oncokb-annotator/MafAnnotator.py -h || exit 1
%environment
export PATH="/opt/samtools:/opt/htslib:/opt/vcf2maf:/opt/oncokb-annotator:/opt/ensembl-vep:/usr/local/bin:$PATH"
export LANG=C.UTF-8
export LC_ALL=C.UTF-8