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##############################################################
# Dockerfile Version: 1.2
# Software: STARK
# Software Version: 3
# Software Website: https://gitlab.bioinfo-diag.fr/Strasbourg/STARK
# Licence: GNU Affero General Public License (AGPL)
# Description: STARK
# Usage: docker run -ti [-v [DATA FOLDER]:/data -v [DATABASE_FOLDER]:/databases] stark:version
##############################################################
##########
# README #
##########
# Config parameters
# identify yum packages for installation
# identify yum packages to remove
#
# Dependecies installation
# identify tools dependences
# config each tool
# write installation procedure for each tools
#
# Tool
# configure tool
# write isntallation procedure for the tool
# add link to current and root tool folder
#
# Workdir / Entrypoint / Cmd
# configure workdir, endpoint and command
# /!\ no variables in endpoint
########
# FROM #
########
FROM centos:7
LABEL Software="STARK" \
Version="0.9.18.5" \
Website="https://gitlab.bioinfo-diag.fr/Strasbourg/STARK" \
maintainer="Antony Le Bechec <antony.lebechec@gmail.com>" \
Description="STARK" \
License="GNU Affero General Public License (AGPL)" \
Usage="docker run [-v [DATA FOLDER]:/STARK/data -v [DATABASE FOLDER]:/STARK/databases -v [RESULTS FOLDER]:/STARK/output/results -v [RUNS FOLDER]:/STARK/input/runs -v [MANIFESTS FOLDER]:/STARK/input/manifests] stark:version"
########
# ARGS #
########
ARG THREADS="1"
# REPO from GIT
ARG REPO_SOURCES="https://gitlab.bioinfo-diag.fr/Strasbourg/STARK-repo/raw/master/"
# REPO from internal HTTP server
#ARG REPO="http://192.168.1.14:8080/"
# REPO null
#ARG REPO=""
ARG REMOVE_SOURCES="1"
##############
# PARAMETERS #
##############
ENV STARK_FOLDER="/STARK"
ENV TOOLS="$STARK_FOLDER/tools"
ENV DATA="$STARK_FOLDER/data"
ENV TOOL="$STARK_FOLDER/tool"
ENV REPO="$REPO_SOURCES"
ENV SOURCES_FOLDER="sources"
ENV SOURCES="$STARK_FOLDER/$SOURCES_FOLDER"
ENV DATABASES="$STARK_FOLDER/databases"
ENV WORKDIR="/tmp"
#ENV YUM_PARAM=" -q -e 0 "
ENV YUM_PARAM=" "
ENV WGET_PARAM=" "
ENV TAR_PARAM=" "
ENV ZIP_PARAM=" "
ENV MAKE_PARAM=" "
###########
# SOURCES #
###########
# Copy sources packages, scripts and tools
ADD ./sources $SOURCES/sources
###########
# WORKDIR #
###########
WORKDIR $WORKDIR
##########
# HEADER #
##########
RUN echo "#[INFO] STARK installation configuration" && \
echo "#[INFO] STARK_FOLDER=$STARK_FOLDER" && \
echo "#[INFO] TOOLS=$TOOLS" && \
echo "#[INFO] DATA=$DATA" && \
echo "#[INFO] TOOL=$TOOL" && \
echo "#[INFO] SOURCES_FOLDER=$SOURCES_FOLDER" && \
echo "#[INFO] SOURCES=$SOURCES" && \
echo "#[INFO] DATABASES=$DATABASES" && \
echo "#[INFO] WORKDIR=$WORKDIR" && \
echo "#[INFO] REMOVE_SOURCES=$REMOVE_SOURCES" && \
echo "#[INFO] THREADS=$THREADS" && \
echo "#[INFO] REPO=$REPO" && \
echo "#";
##################
# SYSTEM INSTALL #
##################
# This will install system packages, python packages and scripts to install tools
ENV YUM_INSTALL="autoconf automake htop bc bzip2 bzip2-devel curl gcc gcc-c++ git lzma lzma-devel make ncurses-devel perl perl-Data-Dumper perl-Digest-MD5 perl-Switch perl-devel perl-Tk tbb-devel unzip rsync wget which xz xz-devel zlib zlib-devel zlib2 zlib2-devel docker java-1.7.0 java-1.8.0 java-11 python2 python2-pip python3 python3-pip python3-devel curl-devel openssl-devel htslib"
#ENV YUM_INSTALL="autoconf automake htop bc bzip2 bzip2-devel curl gcc gcc-c++ git lzma lzma-devel make ncurses-devel perl perl-Data-Dumper perl-Digest-MD5 perl-Switch perl-devel perl-Tk tbb-devel unzip rsync wget which xz xz-devel zlib zlib-devel zlib2 zlib2-devel docker java-1.7.0 java-1.8.0 python2 python2-pip python3 python3-pip python3-devel curl-devel openssl-devel R-core R-core-devel libcurl libcurl-devel libcurl-openssl-devel htslib htslib-devel libxml2-devel"
#ENV YUM_INSTALL_MORE=" R-devel libcurl libcurl-devel libcurl-openssl-devel htslib htslib-devel libxml2-devel perl-Archive-Tar perl-List-MoreUtils"
#ENV YUM_INSTALL_MORE=" R-core R-core-devel libcurl libcurl-devel libcurl-openssl-devel htslib htslib-devel libxml2-devel"
#ENV YUM_INSTALL_MORE=" wget rsync python2 python2-pip python3 python3-pip"
ENV YUM_REMOVE="autoconf automake bzip2-devel lzma-devel ncurses-devel perl-devel tbb-devel xz-devel zlib-devel zlib2-devel python3-devel curl-devel openssl-devel"
#ENV YUM_REMOVE="autoconf automake bzip2-devel lzma-devel ncurses-devel perl-devel tbb-devel xz-devel zlib-devel zlib2-devel python3-devel curl-devel openssl-devel R-core-devel libcurl-devel libcurl-openssl-devel htslib-devel libxml2-devel"
ENV PYTHON_MODULE=""
ENV PYTHON2_MODULE=$PYTHON_MODULE" pathos numpy scipy argparse multiprocess"
ENV PYTHON3_MODULE=$PYTHON_MODULE" pathos numpy scipy argparse"
ENV REPO_SYSTEM_GIT="$REPO/sources.system.tar.gz?path=sources/system"
ENV REPO_SYSTEM_HTTP="$REPO/sources/system/"
ENV REPO_PYTHON_GIT="$REPO/sources.python.tar.gz?path=sources/python"
ENV REPO_PYTHON_HTTP="$REPO/sources/python/"
ENV GET_TOOL_SOURCE=$SOURCES/$SOURCES_FOLDER/get_tool_source.sh
ENV TOOL_INIT=$SOURCES/$SOURCES_FOLDER/tool_init.sh
ENV TOOL_CHECK=$SOURCES/$SOURCES_FOLDER/tool_check.sh
RUN echo "#[INFO] Sources scripts" && \
if [ -e $GET_TOOL_SOURCE ]; then \
echo "#[INFO] GET TOOL SOURCE script exists" ; \
elif $(wget --no-cache --progress=bar:force -nv --quiet "$REPO/$SOURCES_FOLDER/$(basename $GET_TOOL_SOURCE)" -O $GET_TOOL_SOURCE); then \
echo "#[INFO] GET TOOL SOURCE script downloaded from REPO '$REPO/$SOURCES_FOLDER/$(basename $GET_TOOL_SOURCE)'" ; \
else \
mkdir -p $(dirname $GET_TOOL_SOURCE) ; \
echo 'echo "#[INFO] TOOL source ($TOOL_SOURCE)" && \
mkdir -p $(dirname $TOOL_SOURCE) && \
if [ -e $TOOL_SOURCE ]; then \
echo "#[INFO] TOOL TARBALL already in $TOOL_SOURCE"; \
elif $(wget --no-cache --progress=bar:force "$TOOL_SOURCE_REPO" -O $TOOL_SOURCE); then \
echo "#[INFO] TOOL TARBALL downloaded from STARK REPO $TOOL_SOURCE_REPO"; \
if $(wget --no-cache --progress=bar:force -nv --quiet "$(dirname $TOOL_SOURCE_REPO)/source.info" -O $(dirname $TOOL_SOURCE)/source.info); then \
echo "#[INFO] TOOL TARBALL external source information downloaded from STARK REPO $TOOL_SOURCE_REPO " ; \
fi ; \
elif $(wget --no-cache --progress=bar:force "$TOOL_SOURCE_EXTERNAL" -O $TOOL_SOURCE); then \
echo "#[INFO] TOOL TARBALL downloaded from EXTERNAL SOURCE $TOOL_SOURCE_EXTERNAL"; \
echo "$TOOL_SOURCE_EXTERNAL" > $(dirname $TOOL_SOURCE)/source.info; \
else \
echo "#[ERROR] TOOL TARBALL NOT FOUND"; \
exit 1; \
fi && \
if [ -e $(dirname $TOOL_SOURCE)/source.info ]; then \
echo "#[INFO] TOOL TARBALL external source: "$(cat $(dirname $TOOL_SOURCE)/source.info) ; \
fi && \
exit 0;' > $GET_TOOL_SOURCE ; \
echo "#[INFO] GET TOOL SOURCE script written" ; \
fi && \
chmod u+x $GET_TOOL_SOURCE && \
if [ -e $TOOL_INIT ]; then \
echo "#[INFO] TOOL INIT script exists" ; \
elif $(wget --no-cache --progress=bar:force -nv --quiet "$REPO/$SOURCES_FOLDER/$(basename $TOOL_INIT)" -O $TOOL_INIT); then \
echo "#[INFO] TOOLS INIT script downloaded from REPO '$REPO/$SOURCES_FOLDER/$(basename $TOOL_INIT)'" ; \
else \
mkdir -p $(dirname $TOOL_INIT) ; \
echo 'echo "#[INFO] TOOL $TOOL_NAME/$TOOL_VERSION" && \
export TOOL_SOURCE=$SOURCES/$SOURCES_FOLDER/tools/$TOOL_NAME/$TOOL_VERSION/$TOOL_TARBALL && \
export TOOL_SOURCE_REPO=$REPO/$SOURCES_FOLDER/tools/$TOOL_NAME/$TOOL_VERSION/$TOOL_TARBALL && \
export TOOL_SOURCE_BUILD=$SOURCES/$SOURCES_FOLDER/tools/$TOOL_NAME/$TOOL_VERSION/build && \
export TOOL_DEST=$TOOLS/$TOOL_NAME/$TOOL_VERSION && \
export PATH=$TOOL_DEST/bin:$PATH && \
# Get TOOL SOURCE && \
$GET_TOOL_SOURCE $TOOL_SOURCE $TOOL_SOURCE_REPO $TOOL_SOURCE_EXTERNAL && \
# TOOL folder preparation \
echo "#[INFO] TOOL preparation" && \
mkdir -p $TOOL_SOURCE_BUILD && \
mkdir -p $TOOL_DEST/bin && \
echo "#[INFO] TOOL release as current (forced)" && \
ln -snf $TOOL_VERSION/ $TOOLS/$TOOL_NAME/previous && \
if [ -e $TOOLS/$TOOL_NAME/current ]; then ln -snf $(basename $(realpath $TOOLS/$TOOL_NAME/current))/ $TOOLS/$TOOL_NAME/previous; fi && \
ln -snf $TOOL_VERSION/ $TOOLS/$TOOL_NAME/current && \
ln -snf $TOOL_VERSION/ $TOOLS/$TOOL_NAME/latest' > $TOOL_INIT ; \
echo "#[INFO] TOOLS INIT script written" ; \
fi && \
chmod u+x $TOOL_INIT && \
if [ -e $TOOL_CHECK ]; then \
echo "#[INFO] TOOLS CHECK script exists" ; \
elif $(wget --no-cache --progress=bar:force -nv --quiet "$REPO/$SOURCES_FOLDER/$(basename $TOOL_CHECK)" -O $TOOL_CHECK); then \
echo "#[INFO] TOOLS CHECK script downloaded from REPO '$REPO/$SOURCES_FOLDER/$(basename $TOOL_CHECK)'" ; \
else \
mkdir -p $(dirname $TOOL_CHECK) ; \
echo 'echo "#[INFO] TOOL cleaning" && \
rm -rf $TOOL_SOURCE_BUILD && \
if (($REMOVE_SOURCES)); then rm -rf $SOURCES/$SOURCES_FOLDER/tools/$TOOL_NAME/$TOOL_VERSION; fi && \
echo "#[INFO] TOOL $TOOL_NAME/$TOOL_VERSION installed" ;' > $TOOL_CHECK ; \
echo "#[INFO] TOOLS CHECK script written" ; \
fi && \
chmod u+x $TOOL_CHECK && \
echo "#";
# System isntallation
RUN echo "#[INFO] System YUM installation - and download" && \
# Create system repository \
mkdir -p $SOURCES/$SOURCES_FOLDER/system && \
# INSTALL WGET \
echo "#[INFO] System install wget package" && \
#ls $SOURCES/$SOURCES_FOLDER/system/*.rpm && \
if ! ls $SOURCES/$SOURCES_FOLDER/system/wget-*.rpm 1> /dev/null 2>&1; then \
echo "#[INFO] System wget package not locally available"; \
yum $YUM_PARAM install -y --nogpgcheck --downloadonly --downloaddir=$SOURCES/$SOURCES_FOLDER/system/ wget; \
echo "#[INFO] System wget package downloaded from YUM Repository"; \
fi && \
echo "#[INFO] System install rsync package" && \
if ! ls $SOURCES/$SOURCES_FOLDER/system/rsync-*.rpm 1> /dev/null 2>&1; then \
echo "#[INFO] System rsync package not locally available"; \
yum $YUM_PARAM install -y --nogpgcheck --downloadonly --downloaddir=$SOURCES/$SOURCES_FOLDER/system/ rsync; \
echo "#[INFO] System rsync package downloaded from YUM Repository"; \
fi && \
# Install packages locally \
echo "#[INFO] System packages installation locally" && \
yum $YUM_PARAM localinstall -y --nogpgcheck $SOURCES/$SOURCES_FOLDER/system/wget-*.rpm $SOURCES/$SOURCES_FOLDER/system/rsync-*.rpm && \
# Test WGET installation \
if ! command -v wget 1>/dev/null 2>/dev/null; then \
echo "#[ERROR] System wget package not installed (Please open Internet connexion or provide WGET rpm in sources/system folder)"; \
exit 1; \
fi && \
if ! command -v rsync 1>/dev/null 2>/dev/null; then \
echo "#[ERROR] System rsync package not installed (Please open Internet connexion or provide RSYNC rpm in sources/system folder)"; \
exit 1; \
fi && \
# DOWNLOAD packages from repository \
echo "#[INFO] System packages download from REPO '$REPO'"; \
mkdir -p $SOURCES/$SOURCES_FOLDER/system/build && \
# in GIT mode
if wget -q --progress=bar:force --tries=3 $REPO_SYSTEM_GIT -O $SOURCES/$SOURCES_FOLDER/system/build/STARK-repo.sources.system.tar.gz; then \
if tar xf $SOURCES/$SOURCES_FOLDER/system/build/STARK-repo.sources.system.tar.gz -C $SOURCES/$SOURCES_FOLDER/system/build/; then \
rsync -auczqAXhi --no-links --no-perms --no-owner --no-group $SOURCES/$SOURCES_FOLDER/system/build/STARK-repo.sources.system*/sources/system/*rpm $SOURCES/$SOURCES_FOLDER/system/; \
echo "#[INFO] System packages downloaded from REPO '$REPO' (GIT)"; \
else \
echo "#[WARNING] System fail to uncompress packages from REPO '$REPO'"; \
fi; \
# in HTTP mode
elif wget -q --progress=bar:force --tries=3 -r --no-parent $REPO_SYSTEM_HTTP -x --directory-prefix=$SOURCES/$SOURCES_FOLDER/system/build/STARK-repo.sources.system/; then \
rsync -auczqAXhi --no-links --no-perms --no-owner --no-group $SOURCES/$SOURCES_FOLDER/system/build/STARK-repo.sources.system/*/sources/system/*rpm $SOURCES/$SOURCES_FOLDER/system/; \
echo "#[INFO] System packages downloaded from REPO '$REPO' (FTP/HTTP)"; \
else \
echo "#[WARNING] System fail packages download from REPO '$REPO'"; \
fi && \
rm -rf $SOURCES/$SOURCES_FOLDER/system/build && \
# Install packages locally \
echo "#[INFO] System packages installation locally" && \
yum $YUM_PARAM localinstall -y --nogpgcheck $SOURCES/$SOURCES_FOLDER/system/*.rpm && \
# Install EPEL Repository \
echo "#[INFO] System EPEL Repository package" && \
if ! ls $SOURCES/$SOURCES_FOLDER/system/epel-release-*.rpm 1> /dev/null 2>&1; then \
yum $YUM_PARAM install -y --nogpgcheck --downloadonly --downloaddir=$SOURCES/$SOURCES_FOLDER/system/ epel-release; \
echo "#[INFO] System EPEL Repository package downloaded from YUM repository"; \
fi && \
if ls $SOURCES/$SOURCES_FOLDER/system/epel-release-*.rpm 1> /dev/null 2>&1; then \
yum $YUM_PARAM localinstall -y --nogpgcheck $SOURCES/$SOURCES_FOLDER/system/epel-release-*.rpm; \
echo "#[INFO] System EPEL Repository package enabled"; \
else \
echo "#[WARNING] System fail enable EPEL Repository"; \
fi && \
# Update YUM \
echo "#[INFO] System packages update from YUM Repository" && \
mkdir -p $SOURCES/$SOURCES_FOLDER/system/build/update && \
yum $YUM_PARAM update -y --downloadonly --downloaddir=$SOURCES/$SOURCES_FOLDER/system/build/update && \
yum $YUM_PARAM update -y && \
#yum $YUM_PARAM localinstall -y --nogpgcheck $SOURCES/$SOURCES_FOLDER/system/build/update/*.rpm && \
rsync -auczqAXhi --no-links --no-perms --no-owner --no-group $SOURCES/$SOURCES_FOLDER/system/build/update/*rpm $SOURCES/$SOURCES_FOLDER/system/ && \
echo "#[INFO] System packages downloaded & updated from YUM Repository"; \
echo "#[INFO] System packages install from YUM Repository" && \
mkdir -p $SOURCES/$SOURCES_FOLDER/system/build/install && \
yum $YUM_PARAM install -y --downloadonly --downloaddir=$SOURCES/$SOURCES_FOLDER/system/build/install/ $YUM_INSTALL && \
yum $YUM_PARAM install -y $YUM_INSTALL && \
#yum $YUM_PARAM localinstall -y --nogpgcheck $SOURCES/$SOURCES_FOLDER/system/build/install/*.rpm && \
rsync -auczqAXhi --no-links --no-perms --no-owner --no-group $SOURCES/$SOURCES_FOLDER/system/build/install/*rpm $SOURCES/$SOURCES_FOLDER/system/ && \
echo "#[INFO] System packages downloaded & installed from YUM Repository" && \
rm -rf $SOURCES/$SOURCES_FOLDER/system/build && \
yum clean -y all && \
rm -rf /var/cache/yum && \
echo "#[INFO] System Clean" && \
echo "#";
#############
# PYTHON3.9 #
#############
# ENV TOOL_NAME="python"
# ENV TOOL_VERSION="3.9.6"
# ENV TOOL_VERSION_SIMPLE="3.9"
# ENV TOOL_TARBALL="Python-$TOOL_VERSION.tgz"
# ENV TOOL_SOURCE_EXTERNAL="https://www.python.org/ftp/$TOOL_NAME/$TOOL_VERSION/$TOOL_TARBALL"
# ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
# #yum install -y $YUM_INSTALL && \
# source $TOOL_INIT && \
# tar xf $TOOL_SOURCE -C $TOOL_SOURCE_BUILD && \
# echo "whereis gcc" && whereis gcc && \
# (cd $TOOL_SOURCE_BUILD/Python-$TOOL_VERSION && ./configure --enable-optimizations) && \
# make install --quiet -j $THREADS -C $(ls -d $TOOL_SOURCE_BUILD/*) prefix=$TOOL_DEST && \
# ln -sfn $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/pip3 /usr/bin/pip$TOOL_VERSION_SIMPLE && \
# ln -sfn $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/python3 /usr/bin/python$TOOL_VERSION_SIMPLE && \
# # ln -sfn /usr/bin/pip$TOOL_VERSION_SIMPLE /usr/bin/pip3 && \
# # ln -sfn /usr/bin/pip$TOOL_VERSION_SIMPLE /usr/bin/pip && \
# # ln -sfn /usr/bin/python$TOOL_VERSION_SIMPLE /usr/bin/python3 && \
# # ln -sfn /usr/bin/python$TOOL_VERSION_SIMPLE /usr/bin/python && \
# # ln -sfn $TOOL_VERSION $TOOLS/$TOOL_NAME/current ;
# /usr/local/bin/python3.9
# tar xzf Python-3.9.1.tgz
# cd Python-3.9.1
# ./configure --enable-optimizations
# sudo make altinstall
# sudo ln -sfn /usr/local/bin/python3.9 /usr/bin/python3.9
# sudo ln -sfn /usr/local/bin/pip3.9 /usr/bin/pip3.9
# mkdir -p $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin && \
# ln -s /usr/bin/python3 $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/python3 && \
# ln -s python3 $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/python && \
# ln -s /usr/bin/pip3 $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/pip3 && \
# ln -s pip3 $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/pip && \
# ln -s $TOOL_VERSION $TOOLS/$TOOL_NAME/current ;
# wget https://www.python.org/ftp/python/3.7.11/Python-3.7.11.tgz
# PYTHON installation
RUN echo "#[INFO] System Python packages installation - download from REPO '$REPO'"; \
mkdir -p $SOURCES/$SOURCES_FOLDER/python/build && \
# in GIT mode
if wget --progress=bar:force --tries=3 $REPO_PYTHON_GIT -O $SOURCES/$SOURCES_FOLDER/python/build/STARK-repo.sources.python.tar.gz; then \
if tar xf $SOURCES/$SOURCES_FOLDER/python/build/STARK-repo.sources.python.tar.gz -C $SOURCES/$SOURCES_FOLDER/python/build/; then \
rsync -auczqAXhi --no-links --no-perms --no-owner --no-group $SOURCES/$SOURCES_FOLDER/python/build/STARK-repo.sources.python*/sources/system/* $SOURCES/$SOURCES_FOLDER/python/; \
echo "#[INFO] System Python packages downloaded from REPO '$REPO' (GIT)"; \
else \
echo "#[WARNING] System fail to uncompress Python packages from REPO '$REPO'"; \
fi; \
# in HTTP mode
elif wget --progress=bar:force --tries=3 -r --no-parent $REPO_PYTHON_HTTP -x --directory-prefix=$SOURCES/$SOURCES_FOLDER/python/build/STARK-repo.sources.system/; then \
rsync -auczqAXhi --no-links --no-perms --no-owner --no-group $SOURCES/$SOURCES_FOLDER/system/build/STARK-repo.sources.system*/sources/python/* $SOURCES/$SOURCES_FOLDER/python/; \
echo "#[INFO] System Python packages downloaded from REPO '$REPO' (FTP/HTTP)"; \
else \
echo "#[WARNING] System fail Python packages download from REPO '$REPO'"; \
fi && \
rm -rf $SOURCES/$SOURCES_FOLDER/python/build && \
# Install Python packages locally \
echo "#[INFO] System Python packages installation locally" && \
if ls $SOURCES/$SOURCES_FOLDER/python/2/*whl 1> /dev/null 2>&1; then \
pip2 --no-cache-dir install $SOURCES/$SOURCES_FOLDER/python/2/*whl ; \
fi && \
if ls $SOURCES/$SOURCES_FOLDER/python/3/*whl 1> /dev/null 2>&1; then \
pip3 --no-cache-dir install $SOURCES/$SOURCES_FOLDER/python/3/*whl ; \
fi && \
# Update PIP \
echo "#[INFO] System Python packages update from PIP Repository" && \
echo "#[INFO] System Python packages update from PIP Repository - Python2" && \
mkdir -p $TOOLS/python/2/bin && \
mkdir -p $SOURCES/$SOURCES_FOLDER/python/2 && \
if [ ! -e $SOURCES/$SOURCES_FOLDER/python/2/get-pip.py ]; then \
curl https://bootstrap.pypa.io/pip/2/get-pip.py --output $SOURCES/$SOURCES_FOLDER/python/2/get-pip.py; \
fi && \
if [ -e $SOURCES/$SOURCES_FOLDER/python/2/get-pip.py ]; then \
cp $SOURCES/$SOURCES_FOLDER/python/2/get-pip.py $TOOLS/python/2/bin/get-pip.py; \
chmod u+x $TOOLS/python/2/bin/get-pip.py; \
else \
echo "#[ERROR] No Python2 get-pip.py"; \
exit 1; \
fi && \
$TOOLS/python/2/bin/get-pip.py && \
python2 -m pip --no-cache-dir install --upgrade pip && \
echo "#[INFO] System Python packages update from PIP Repository - Python3" && \
python3 -m pip --no-cache-dir install --upgrade pip && \
echo "#[INFO] System Python packages downloaded & updated from PIP Repository" && \
echo "#[INFO] System Python packages install from PIP Repository" && \
echo "#[INFO] System Python packages install from PIP Repository - Python2" && \
if (( $(echo $PYTHON2_MODULE | wc -w | tr -d " ") )); then \
python2 -m pip --no-cache-dir download $PYTHON2_MODULE --dest $SOURCES/$SOURCES_FOLDER/python/2/ ; \
python2 -m pip --no-cache-dir install $SOURCES/$SOURCES_FOLDER/python/2/*whl ; \
fi && \
echo "#[INFO] System Python packages install from PIP Repository - Python3" && \
if (( $(echo $PYTHON3_MODULE | wc -w | tr -d " ") )); then \
python3 -m pip --no-cache-dir download $PYTHON3_MODULE --dest $SOURCES/$SOURCES_FOLDER/python/3/ ; \
python3 -m pip --no-cache-dir install $SOURCES/$SOURCES_FOLDER/python/3/*whl ; \
fi && \
echo "#[INFO] System Python packages downloaded & installed from PIP Repository" && \
# CLEAN
echo "#[INFO] System Cleaning" && \
if (($REMOVE_SOURCES)); then \
rm -rf $SOURCES/$SOURCES_FOLDER/system $SOURCES/$SOURCES_FOLDER/python ; \
echo "#[INFO] System Remove Sources" ; \
fi && \
echo "#[INFO] System Clean" && \
echo "#";
#####
# R #
#####
## Install R packages
# RUN echo "#[INFO] System R packages installation" && \
# R -e "install.packages(c('BiocManager', 'devtools', 'stringr' ,'optparse'), dependencies=TRUE, repos = 'http://cran.us.r-project.org')" && \
# R -e 'BiocManager::install(ask = F)' && R -e 'BiocManager::install(c("Biostrings", "Rsamtools", ask = F))' && \
# echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile && \
# Rscript -e "library(devtools); install_github('mhahsler/rBLAST')"
# RUN echo "#[INFO] System R packages installation" && \
# R -e "install.packages(c('--no-docs', '--no-help', '--no-html', 'BiocManager', 'devtools', 'stringr' ,'optparse'), dependencies=TRUE, repos = 'http://cran.us.r-project.org')" && \
# R -e 'BiocManager::install(ask = F)' && R -e 'BiocManager::install(c("Biostrings", "Rsamtools", ask = F))'
################
# DEPENDENCIES #
################
### TOOL INSTALLATION CODE FORMAT
# All variables <VARIABLE> must be changed
# ##########
# # <TOOL> #
# ##########
#
# # TOOL INFO
# ENV TOOL_NAME="<TOOL_NAME>" # tool name
# ENV TOOL_VERSION="<TOOL_RELEASE>" # tool release
# ENV TOOL_TARBALL="<TOOL_TARBALL>" # filename of the tarball
# ENV TOOL_SOURCE_EXTERNAL="<TOOL_SOURCE_EXTERNAL>" # Extenal tarball source of the tool
# ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH # Add tool bin to the PATH
# # TOOL PARAMETERS
# ENV TOOL_PARAM_<VARIABLE1>="<VALUE1>" # Parameter 1
# ENV TOOL_PARAM_<VARIABLE2>="<VALUE2>" # Parameter 2
#
# # TOOL INSTALLATION
# RUN source $TOOL_INIT && \ # Init tool variables && tarball source && ...
# echo "#[INFO] TOOL installation" && \ # head
# <Installation CMD such as tar... && cp... && ...> && \ # Installation commands using $TOOL_SOURCE $TOOL_SOURCE_BUILD $TOOL_DEST...
# # Example: tar && make install \ # Example of command (tar && make install)
# tar xf $TOOL_SOURCE -C $TOOL_SOURCE_BUILD && \
# make install -j $THREADS -C $(ls -d $TOOL_SOURCE_BUILD/*) prefix=$TOOL_DEST && \
# # Example: unzip && rpm \ # Example of command (unzip && rpm)
# unzip -q $TOOL_SOURCE -d $TOOL_SOURCE_BUILD && \
# rpm -ih $TOOL_SOURCE_BUILD/*.rpm --excludedocs --prefix=$TOOL_DEST && \
# $TOOL_CHECK ; # Check tool, rm source build folder...
################
# TOOLS SYSTEM #
################
#########
# JAVA7 #
#########
ENV TOOL_NAME="java"
ENV TOOL_VERSION="1.7.0"
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
mkdir -p $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin && \
ln -s /usr/lib/jvm/jre-1.7.0/bin/java $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/java ;
##########
# JAVA11 #
##########
ENV TOOL_NAME="java"
ENV TOOL_VERSION="11"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
mkdir -p $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin && \
ln -s /usr/lib/jvm/jre-11/bin/java $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/java ;
#########
# JAVA8 #
#########
ENV TOOL_NAME="java"
ENV TOOL_VERSION="1.8.0"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
mkdir -p $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin && \
ln -s /usr/lib/jvm/jre-1.8.0/bin/java $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/java && \
ln -s $TOOL_VERSION $TOOLS/$TOOL_NAME/current ;
###########
# PYTHON2 #
###########
ENV TOOL_NAME="python"
ENV TOOL_VERSION="2"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
mkdir -p $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin && \
ln -s /usr/bin/python2 $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/python2 && \
ln -s python2 $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/python && \
ln -s /usr/bin/pip2 $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/pip2 && \
ln -s pip2 $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/pip ;
###########
# PYTHON3 #
###########
ENV TOOL_NAME="python"
ENV TOOL_VERSION="3"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
mkdir -p $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin && \
ln -s /usr/bin/python3 $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/python3 && \
ln -s python3 $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/python && \
ln -s /usr/bin/pip3 $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/pip3 && \
ln -s pip3 $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/pip && \
ln -s $TOOL_VERSION $TOOLS/$TOOL_NAME/current ;
################
# TOOLS EXTERN #
################
##########
# PATHOS #
##########
# # TOOL INFO
# ENV TOOL_NAME="pathos"
# ENV TOOL_VERSION="master"
# ENV TOOL_TARBALL="$TOOL_VERSION.tar.gz"
# ENV TOOL_SOURCE_EXTERNAL="https://github.com/uqfoundation/pathos/archive/$TOOL_TARBALL"
# ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# # TOOL PARAMETERS
# ENV TOOL_TARBALL_FOLDER="$TOOL_NAME-$TOOL_VERSION"
# # TOOL INSTALLATION
# RUN source $TOOL_INIT && \
# echo "#[INFO] TOOL installation" && \
# tar xf $TOOL_SOURCE -C $TOOL_SOURCE_BUILD && \
# echo "#[INFO] TOOL installation - python2 setup.py build" && \
# (cd $TOOL_SOURCE_BUILD/$TOOL_TARBALL_FOLDER/; python2 setup.py build) && \
# echo "#[INFO] TOOL installation - python2 setup.py install" && \
# (cd $TOOL_SOURCE_BUILD/$TOOL_TARBALL_FOLDER/; python2 setup.py install) && \
# $TOOL_CHECK ;
#echo "#[INFO] TOOL installation - pip2 install" && \
# pip2 install pathos==0.2.6 && \
###########
# ANNOVAR #
###########
# TOOL INFO
ENV TOOL_NAME="annovar"
ENV TOOL_VERSION="2020Jun08"
ENV TOOL_TARBALL="$TOOL_NAME.latest.tar.gz"
ENV TOOL_SOURCE_EXTERNAL="http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/$TOOL_TARBALL"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# TOOL PARAMETERS
ENV TOOL_PARAM_TARBALL_FOLDER=$TOOL_NAME
ENV TOOL_PARAM_DATABASE_FOLDER_LINK=$DATABASES/annovar/current
ENV TOOL_PARAM_DATABASE_FOLDER=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/databases/
# TOOL INSTALLATION
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
source $TOOL_INIT && \
tar xf $TOOL_SOURCE -C $TOOL_SOURCE_BUILD && \
cp $TOOL_SOURCE_BUILD/*/*.pl $TOOL_DEST/bin/ -R && \
echo "#[INFO] TOOL databases configuration" && \
mkdir -p $TOOL_PARAM_DATABASE_FOLDER_LINK && \
mkdir -p $TOOL_PARAM_DATABASE_FOLDER && \
ln -s $TOOL_PARAM_DATABASE_FOLDER_LINK $TOOL_PARAM_DATABASE_FOLDER && \
$TOOL_CHECK ;
#############
# BLAST+ #
#############
# https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.12.0+-1.x86_64.rpm
# https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.12.0+-x64-linux.tar.gz
# blastn, blastp, blastx, and makeblastdb
# # TOOL INFO
# ENV TOOL_NAME="ncbi-blast"
# ENV TOOL_VERSION="2.12.0"
# ENV TOOL_TARBALL=$TOOL_NAME-$TOOL_VERSION"+-x64-linux.tar.gz"
# ENV TOOL_SOURCE_EXTERNAL="https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/$TOOL_TARBALL"
# ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# # TOOL PARAMETERS
# # TOOL INSTALLATION
# RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
# source $TOOL_INIT && \
# tar xf $TOOL_SOURCE -C $TOOL_SOURCE_BUILD && \
# cp -R $TOOL_SOURCE_BUILD/*/* $TOOL_DEST/ && \
# chmod a+x $TOOL_DEST/bin/* && \
# $TOOL_CHECK ;
##########
# HTSLIB #
##########
# TOOL INFO
ENV TOOL_NAME="htslib"
ENV TOOL_VERSION="1.15.1"
ENV TOOL_TARBALL="$TOOL_NAME-$TOOL_VERSION.tar.bz2"
ENV TOOL_SOURCE_EXTERNAL="https://github.com/samtools/$TOOL_NAME/releases/download/$TOOL_VERSION/$TOOL_TARBALL"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# TOOL PARAMETERS
# TOOL INSTALLATION
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
source $TOOL_INIT && \
tar xf $TOOL_SOURCE -C $TOOL_SOURCE_BUILD && \
make install --quiet -j $THREADS -C $(ls -d $TOOL_SOURCE_BUILD/*) prefix=$TOOL_DEST && \
$TOOL_CHECK ;
############
# BCFTOOLS #
############
# TOOL INFO
ENV TOOL_NAME="bcftools"
ENV TOOL_VERSION="1.15.1"
ENV TOOL_TARBALL="$TOOL_NAME-$TOOL_VERSION.tar.bz2"
ENV TOOL_SOURCE_EXTERNAL="https://github.com/samtools/$TOOL_NAME/releases/download/$TOOL_VERSION/$TOOL_TARBALL"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# TOOL PARAMETERS
# TOOL INSTALLATION
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
source $TOOL_INIT && \
tar xf $TOOL_SOURCE -C $TOOL_SOURCE_BUILD && \
make install --quiet -j $THREADS -C $(ls -d $TOOL_SOURCE_BUILD/*) prefix=$TOOL_DEST && \
$TOOL_CHECK ;
#############
# BCL2FASTQ #
#############
# TOOL INFO
ENV TOOL_NAME="bcl2fastq"
ENV TOOL_VERSION="2.20.0"
ENV TOOL_TARBALL=$TOOL_NAME"2-v2-20-0-linux-x86-64.zip"
ENV TOOL_SOURCE_EXTERNAL="https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/$TOOL_TARBALL"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# TOOL PARAMETERS
# TOOL INSTALLATION
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
source $TOOL_INIT && \
unzip -q $TOOL_SOURCE -d $TOOL_SOURCE_BUILD && \
rpm -ih $TOOL_SOURCE_BUILD/*.rpm --excludedocs --prefix=$TOOL_DEST && \
$TOOL_CHECK ;
############
# BEDTOOLS #
############
# TOOL INFO
ENV TOOL_NAME="bedtools"
ENV TOOL_VERSION="2.30.0"
ENV TOOL_TARBALL="$TOOL_NAME-$TOOL_VERSION.tar.gz"
ENV TOOL_SOURCE_EXTERNAL="https://github.com/arq5x/bedtools2/releases/download/v$TOOL_VERSION/$TOOL_TARBALL"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# TOOL PARAMETERS
# TOOL INSTALLATION
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
source $TOOL_INIT && \
tar xf $TOOL_SOURCE -C $TOOL_SOURCE_BUILD && \
make install --quiet -j $THREADS -C $(ls -d $TOOL_SOURCE_BUILD/*) prefix=$TOOL_DEST && \
$TOOL_CHECK ;
############
# BOWTIE2 #
############
# TOOL INFO
ENV TOOL_NAME="bowtie2"
ENV TOOL_VERSION="2.4.5"
ENV TOOL_TARBALL="$TOOL_NAME-$TOOL_VERSION-linux-x86_64.zip"
ENV TOOL_SOURCE_EXTERNAL="https://github.com/BenLangmead/bowtie2/releases/download/v$TOOL_VERSION/$TOOL_TARBALL"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# TOOL PARAMETERS
# TOOL INSTALLATION
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
source $TOOL_INIT && \
unzip -q $TOOL_SOURCE -d $TOOL_SOURCE_BUILD && \
cp $TOOL_SOURCE_BUILD/*/bowtie2* $TOOL_DEST/bin/ && \
rm -f $TOOL_DEST/bin/*debug && \
$TOOL_CHECK ;
#######
# BWA #
#######
# TOOL INFO
ENV TOOL_NAME="bwa"
ENV TOOL_VERSION="0.7.17"
ENV TOOL_TARBALL="$TOOL_NAME-$TOOL_VERSION.tar.bz2"
ENV TOOL_SOURCE_EXTERNAL="https://sourceforge.net/projects/bio-bwa/files/$TOOL_NAME-$TOOL_VERSION.tar.bz2/download"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# TOOL PARAMETERS
# TOOL INSTALLATION
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
source $TOOL_INIT && \
tar xf $TOOL_SOURCE -C $TOOL_SOURCE_BUILD && \
make --quiet -j $THREADS -C $(ls -d $TOOL_SOURCE_BUILD/*) && \
cp $TOOL_SOURCE_BUILD/*/bwa $TOOL_DEST/bin/ && \
$TOOL_CHECK ;
#########
# FASTP #
#########
# TOOL INFO
ENV TOOL_NAME="fastp"
ENV TOOL_VERSION="0.23.2"
ENV TOOL_TARBALL="$TOOL_NAME"
ENV TOOL_SOURCE_EXTERNAL="http://opengene.org/$TOOL_NAME/$TOOL_NAME.$TOOL_VERSION"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# TOOL PARAMETERS
# TOOL INSTALLATION
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
source $TOOL_INIT && \
cp $TOOL_SOURCE $TOOL_DEST/bin/ && \
chmod a+x $TOOL_DEST/bin/* && \
$TOOL_CHECK ;
#######
# CAP #
#######
# TOOL INFO
ENV TOOL_NAME="cap"
ENV TOOL_VERSION="0.9.13"
ENV TOOL_TARBALL="$TOOL_VERSION.tar.gz"
ENV TOOL_SOURCE_EXTERNAL="https://github.com/bioinfo-chru-strasbourg/CAP/archive/refs/heads/$TOOL_TARBALL"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# TOOL PARAMETERS
# TOOL INSTALLATION
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
source $TOOL_INIT && \
tar xf $TOOL_SOURCE -C $TOOL_SOURCE_BUILD && \
cp -R $TOOL_SOURCE_BUILD/*/* $TOOL_DEST/ && \
chmod a+x $TOOL_DEST/bin/* && \
$TOOL_CHECK ;
#########
# GATK4 #
#########
# TOOL INFO
ENV TOOL_NAME="gatk"
#ENV TOOL_VERSION="4.1.9.0"
ENV TOOL_VERSION="4.2.6.1"
ENV TOOL_TARBALL="gatk-$TOOL_VERSION.zip"
ENV TOOL_SOURCE_EXTERNAL="https://github.com/broadinstitute/gatk/releases/download/$TOOL_VERSION/$TOOL_TARBALL"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# TOOL PARAMETERS
ENV TOOL_JAR=gatk-package-$TOOL_VERSION-local.jar
# TOOL INSTALLATION
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
source $TOOL_INIT && \
unzip -q $TOOL_SOURCE -d $TOOL_SOURCE_BUILD && \
cp -R $TOOL_SOURCE_BUILD/gatk-$TOOL_VERSION/* $TOOL_DEST/bin/ && \
$TOOL_CHECK ;
########
# GATK #
########
# TOOL INFO
ENV TOOL_NAME="gatk"
ENV TOOL_VERSION="3.8-1-0"
ENV TOOL_TARBALL="GenomeAnalysisTK-$TOOL_VERSION.tar.bz2"
ENV TOOL_SOURCE_EXTERNAL="https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=$TOOL_VERSION-gf15c1c3ef"
#ENV TOOL_SOURCE_EXTERNAL="https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-$TOOL_VERSION-gf15c1c3ef.tar.bz2"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# TOOL PARAMETERS
ENV TOOL_JAR=GenomeAnalysisTK.jar
# TOOL INSTALLATION
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
source $TOOL_INIT && \
tar xf $TOOL_SOURCE -C $TOOL_SOURCE_BUILD && \
cp -R $TOOL_SOURCE_BUILD/*/$TOOL_JAR $TOOL_DEST/bin/ && \
$TOOL_CHECK ;
##########
# HOWARD #
##########
# TOOL INFO
ENV TOOL_NAME="howard"
ENV TOOL_VERSION="0.9.15.6"
ENV TOOL_TARBALL="$TOOL_VERSION.tar.gz"
ENV TOOL_SOURCE_EXTERNAL="https://github.com/bioinfo-chru-strasbourg/howard/archive/refs/heads/$TOOL_TARBALL"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# TOOL PARAMETERS
ENV TOOL_PARAM_DATABASE_FOLDER_LINK=$DATABASES
ENV TOOL_PARAM_DATABASE_FOLDER=/databases
# TOOL INSTALLATION
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
source $TOOL_INIT && \
tar xf $TOOL_SOURCE -C $TOOL_SOURCE_BUILD && \
cp -R $TOOL_SOURCE_BUILD/*/* $TOOL_DEST/ && \
chmod a+x $TOOL_DEST/* -R && \
mkdir -p $TOOL_PARAM_DATABASE_FOLDER_LINK && \
mkdir -p $TOOL_PARAM_DATABASE_FOLDER && \
ln -s $DATABASES $TOOL_DATABASE_FOLDER && \
$TOOL_CHECK ;
############
# IGVTOOLS #
############
# TOOL INFO
ENV TOOL_NAME="igvtools"
ENV TOOL_VERSION="2.4.19"
ENV TOOL_TARBALL="igvtools_$TOOL_VERSION.zip"
ENV TOOL_VERSION_MAIN="2.4"
ENV TOOL_SOURCE_EXTERNAL="http://data.broadinstitute.org/igv/projects/downloads/$TOOL_VERSION_MAIN/$TOOL_TARBALL"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# TOOL PARAMETERS
# TOOL INSTALLATION
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
source $TOOL_INIT && \
unzip -q $TOOL_SOURCE -d $TOOL_SOURCE_BUILD && \
cp -R $TOOL_SOURCE_BUILD/*/* $TOOL_DEST/bin/ && \
$TOOL_CHECK ;
###########
# ITDSEEK #
###########
# TOOL INFO
ENV TOOL_NAME="itdseek"
ENV TOOL_VERSION="1.2-2"
ENV TOOL_TARBALL="$TOOL_NAME-$TOOL_VERSION.zip"
ENV TOOL_SOURCE_EXTERNAL="https://github.com/tommyau/itdseek/zipball/master/$TOOL_TARBALL"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# TOOL PARAMETERS
# TOOL INSTALLATION
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
source $TOOL_INIT && \
unzip -q $TOOL_SOURCE -d $TOOL_SOURCE_BUILD && \
cp -R $TOOL_SOURCE_BUILD/*/* $TOOL_DEST/bin/ && \
$TOOL_CHECK ;
##########
# MUTECT #
##########
# TOOL INFO
ENV TOOL_NAME="mutect"
ENV TOOL_VERSION="1.1.7"
ENV TOOL_TARBALL="$TOOL_NAME-$TOOL_VERSION.jar.zip"
ENV TOOL_SOURCE_EXTERNAL="https://software.broadinstitute.org/gatk/download/auth?package=M1"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# TOOL PARAMETERS
ENV TARBALL_JAR=mutect-$TOOL_VERSION.jar
ENV TOOL_JAR=mutect.jar
# TOOL INSTALLATION
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
source $TOOL_INIT && \
unzip -q $TOOL_SOURCE -d $TOOL_DEST/bin/ && \
mv $TOOL_DEST/bin/$TARBALL_JAR $TOOL_DEST/bin/$TOOL_JAR && \
$TOOL_CHECK ;
############
# OUTLYZER #
############
# TOOL INFO
ENV TOOL_NAME="outlyzer"
ENV TOOL_VERSION="3"
ENV TOOL_TARBALL="outLyzer.py"
ENV TOOL_SOURCE_EXTERNAL="https://raw.githubusercontent.com/EtieM/outLyzer/master/$TOOL_TARBALL"
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# TOOL PARAMETERS
# TOOL INSTALLATION
RUN echo "#[INFO] TOOL installation '$TOOL_NAME:$TOOL_VERSION'" && \
source $TOOL_INIT && \
cp $TOOL_SOURCE -d $TOOL_DEST/bin/ && \
chmod a+x $TOOL_DEST/bin/*.py && \
$TOOL_CHECK ;
##########
# PICARD #
##########
# TOOL INFO