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Dockerfile
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FROM centos
MAINTAINER Antony Le Bechec <[email protected]>
##############################################################
# Dockerfile Version: 1.0
# Software: OUTLYZER
# Software Version: 2
# Software Website: https://github.com/EtieM/outLyzer
# Description: SAMTOOLS
##############################################################
#######
# YUM #
#######
#RUN yum update -y
RUN yum install -y zlib-devel zlib \
zlib2-devel zlib2 \
bzip2-devel bzip2 \
lzma-devel lzma \
xz-devel xz \
ncurses-devel \
wget \
gcc \
python2-pip \
python2-setuptools \
epel-release \
make ;
RUN yum clean all ;
# python2-wheel
##########
# 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
############
# 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
############
# 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
############
# OUTLYSER #
############
ENV TOOLS=/home/TOOLS/tools
ENV TOOL_NAME=outlyzer
ENV TOOL_VERSION=2
ENV FILE_LOCATION=https://raw.githubusercontent.com/EtieM/outLyzer/master
ENV FILE=outLyzer.py
ENV DEST=$TOOLS/$TOOL_NAME/$TOOL_VERSION
ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
RUN yum install -y python2-pip;
RUN pip install --upgrade pip;
RUN wget $FILE_LOCATION/$FILE ; \
mkdir -p $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin ; \
cp $FILE $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/ ;
RUN pip install numpy scipy argparse
RUN cd /
RUN wget https://github.com/uqfoundation/pathos/archive/master.tar.gz ; \
tar -xvzf master.tar.gz ; \
chmod 0775 pathos-master -R ; \
cd pathos-master ; \
python ./setup.py build ; \
python ./setup.py install ; \
cd .. ; \
rm -rf pathos-master ;
# subprocess numpy scipy argparse multiprocessing
#######
# YUM #
#######
RUN yum erase -y zlib-devel \
zlib2-devel \
bzip2-devel \
lzma-devel \
xz-devel \
ncurses-devel \
wget \
gcc \
make ;
RUN yum clean all ;
WORKDIR "$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin"
CMD ["/bin/bash"]