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Dockerfile
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FROM centos
MAINTAINER Antony Le Bechec <[email protected]>
##############################################################
# Dockerfile Version: 1.0
# Software: FATBAM
# Software Version: 0.9.9b
# Software Website: https://gitlab.bioinfo-diag.fr/lebechec/FATBAM
# Description: FATBAM
##############################################################
#######
# YUM #
#######
#RUN yum update -y
RUN yum install -y java-1.8.0 \
zlib-devel zlib \
zlib2-devel zlib2 \
bzip2-devel bzip2 \
lzma-devel lzma \
xz-devel xz \
ncurses-devel \
wget \
gcc \
gcc-c++ \
make \
perl \
perl-Switch \
perl-Digest-MD5 \
perl-Data-Dumper \
bc ;
RUN yum clean all ;
##########
# HTSLIB #
##########
ENV TOOLS=/home/TOOLS/tools
ENV TOOL_NAME=htslib
ENV TOOL_VERSION=1.8
ENV TARBALL_LOCATION=https://github.com/samtools/$TOOL_NAME/releases/download/$TOOL_VERSION/
ENV TARBALL=$TOOL_NAME-$TOOL_VERSION.tar.bz2
ENV DEST=$TOOLS/$TOOL_NAME/$TOOL_VERSION
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# INSTALL
RUN wget $TARBALL_LOCATION/$TARBALL ; \
tar xf $TARBALL ; \
rm -rf $TARBALL ; \
cd $TOOL_NAME-$TOOL_VERSION ; \
make prefix=$TOOLS/$TOOL_NAME/$TOOL_VERSION install ; \
cd ../ ; \
rm -rf $TOOL_NAME-$TOOL_VERSION ; \
ln -s $TOOLS/$TOOL_NAME/$TOOL_VERSION $TOOLS/$TOOL_NAME/current
############
# BCFTOOLS #
############
ENV TOOLS=/home/TOOLS/tools
ENV TOOL_NAME=bcftools
ENV TOOL_VERSION=1.8
ENV TARBALL_LOCATION=https://github.com/samtools/$TOOL_NAME/releases/download/$TOOL_VERSION/
ENV TARBALL=$TOOL_NAME-$TOOL_VERSION.tar.bz2
ENV DEST=$TOOLS/$TOOL_NAME/$TOOL_VERSION
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# INSTALL
RUN wget $TARBALL_LOCATION/$TARBALL ; \
tar xf $TARBALL ; \
rm -rf $TARBALL ; \
cd $TOOL_NAME-$TOOL_VERSION ; \
make prefix=$TOOLS/$TOOL_NAME/$TOOL_VERSION install ; \
cd ../ ; \
rm -rf $TOOL_NAME-$TOOL_VERSION ; \
ln -s $TOOLS/$TOOL_NAME/$TOOL_VERSION $TOOLS/$TOOL_NAME/current
############
# SAMTOOLS #
############
ENV TOOLS=/home/TOOLS/tools
ENV TOOL_NAME=samtools
ENV TOOL_VERSION=1.8
ENV TARBALL_LOCATION=https://github.com/samtools/$TOOL_NAME/releases/download/$TOOL_VERSION/
ENV TARBALL=$TOOL_NAME-$TOOL_VERSION.tar.bz2
ENV DEST=$TOOLS/$TOOL_NAME/$TOOL_VERSION
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# INSTALL
RUN wget $TARBALL_LOCATION/$TARBALL ; \
tar xf $TARBALL ; \
rm -rf $TARBALL ; \
cd $TOOL_NAME-$TOOL_VERSION ; \
make prefix=$TOOLS/$TOOL_NAME/$TOOL_VERSION install ; \
cd ../ ; \
rm -rf $TOOL_NAME-$TOOL_VERSION ; \
ln -s $TOOLS/$TOOL_NAME/$TOOL_VERSION $TOOLS/$TOOL_NAME/current
############
# BEDTOOLS #
############
ENV TOOLS=/home/TOOLS/tools
ENV TOOL_NAME=bedtools
ENV TOOL_VERSION=2.27.1
ENV TARBALL_LOCATION=https://github.com/arq5x/bedtools2/releases/download/v$TOOL_VERSION
ENV TARBALL=$TOOL_NAME-$TOOL_VERSION.tar.gz
ENV TARBALL_FOLDER=bedtools2
ENV DEST=$TOOLS/$TOOL_NAME/$TOOL_VERSION
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# INSTALL
RUN wget $TARBALL_LOCATION/$TARBALL ; \
tar xf $TARBALL ; \
rm -rf $TARBALL ; \
cd $TARBALL_FOLDER ; \
make prefix=$TOOLS/$TOOL_NAME/$TOOL_VERSION install ; \
cd ../ ; \
rm -rf $TARBALL_FOLDER ; \
ln -s $TOOLS/$TOOL_NAME/$TOOL_VERSION $TOOLS/$TOOL_NAME/current ;
##########
# PICARD #
##########
ENV TOOLS /home/TOOLS/tools
ENV TOOL_NAME picard
ENV TOOL_VERSION 2.18.5
ENV JAR_LOCATION https://github.com/broadinstitute/picard/releases/download/$TOOL_VERSION
ENV JAR picard.jar
ENV DEST $TOOLS/$TOOL_NAME/$TOOL_VERSION
ENV PATH "$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH"
# INSTALL
RUN wget $JAR_LOCATION/$JAR ; \
mkdir -p $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin ; \
mv $JAR $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin ; \
ln -s $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/$JAR /$JAR ; \
ln -s $TOOLS/$TOOL_NAME/$TOOL_VERSION $TOOLS/$TOOL_NAME/current ;
##########
# FATBAM #
##########
# https://gitlab.bioinfo-diag.fr/lebechec/FATBAM/repository/0.9.9b/archive.tar.gz
# https://gitlab.bioinfo-diag.fr/lebechec/FATBAM/repository/0.9.9b/archive.tar.gz
ENV TOOLS=/home/TOOLS/tools
ENV TOOL_NAME=fatbam
ENV TOOL_VERSION=0.9.9b
ENV TARBALL_LOCATION=https://gitlab.bioinfo-diag.fr/lebechec/FATBAM/repository/0.9.9b
ENV TARBALL=archive.tar.gz
ENV TARBALL_FOLDER=archive
ENV DEST=$TOOLS/$TOOL_NAME/$TOOL_VERSION
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
# INSTALL
RUN wget $TARBALL_LOCATION/$TARBALL ; \
tar xf $TARBALL ; \
rm -rf $TARBALL ; \
mkdir -p $TOOLS/$TOOL_NAME/$TOOL_VERSION/ ; \
cp $(ls ${TOOL_NAME^^}-$TOOL_VERSION* -d)/* $TOOLS/$TOOL_NAME/$TOOL_VERSION/ -R ; \
rm -rf $(ls ${TOOL_NAME^^}-$TOOL_VERSION* -d) ; \
ln -s $TOOLS/$TOOL_NAME/$TOOL_VERSION $TOOLS/$TOOL_NAME/current ; \
chmod 0775 $TOOLS/$TOOL_NAME/$TOOL_VERSION $TOOLS/$TOOL_NAME/current -R ;
#######
# YUM #
#######
RUN yum erase -y zlib-devel \
zlib2-devel \
bzip2-devel \
lzma-devel \
xz-devel \
ncurses-devel \
wget \
gcc \
gcc-c++ ;
RUN yum clean all ;
WORKDIR "$TOOLS/$TOOL_NAME/current/bin"
CMD ["/bin/bash"]