bioinfochrustrasbourg/controlfreec repository overview

FROM centos MAINTAINER Vincent Zilliox [email protected]⁠

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⁠Dockerfile Version: 1.0

⁠Software: Control FREEK

⁠Software Version: 11.3

⁠Software Website: https://github.com/BoevaLab/FREEC⁠

⁠Description: Dockerfile to build Control FREEK container image

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⁠YUM

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RUN yum install -y epel-release
wget make
zlib-devel zlib
zlib2-devel zlib2
bzip2-devel bzip2
lzma-devel lzma
ncurses-devel ncurses
xz-devel xz
gcc gcc-c++
R perl;

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⁠HTSLIB

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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

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⁠SAMTOOLS

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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 PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/:$PATH

⁠INSTALL

RUN wget $TARBALL_LOCATION/$TARBALL ;
tar xf samtools-1.8.tar.bz2;
rm -rf $TARBALL ;
cd samtools-1.8 ;
make prefix=$TOOLS/$TOOL_NAME/$TOOL_VERSION install ;
cd ../ ;
rm -rf $TOOL_NAME-$TOOL_VERSION ;
ln -s $TOOLS/$TOOL_NAME/$TOOL_VERSION $TOOLS/$TOOL_NAME/current

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⁠BEDTOOLS

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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-$TOOL_VERSION.tar.gz ENV TARBALL_FOLDER=bedtools2 ENV PATH=$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 ;

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⁠sambamba

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ENV TOOLS=/home/TOOLS/tools ENV TOOL_NAME=sambamba ENV TOOL_VERSION=0.6.7 ENV TARBALL_LOCATION=https://github.com/biod/$TOOL_NAME/releases/download/v$TOOL_VERSION⁠ ENV TARBALL=$TOOL_NAME_v$TOOL_VERSION_linux.tar.bz2 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/bin;
mv $TOOL_NAME $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin;
ln -s $TOOLS/$TOOL_NAME/$TOOL_VERSION $TOOLS/$TOOL_NAME/current ;

#################

⁠Control FREEK

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ENV TOOLS=/home/TOOLS/tools ENV TOOL_NAME=FREEC ENV TOOL_VERSION=11.3 ENV TARBALL_LOCATION=https://github.com/BoevaLab/$TOOL_NAME/archive⁠ ENV TARBALL=v$TOOL_VERSION.tar.gz ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/src/:$PATH

⁠INSTALL

RUN wget $TARBALL_LOCATION/$TARBALL ;
tar xf $TARBALL ;
rm -rf $TARBALL ;
mkdir -p $TOOLS/$TOOL_NAME/$TOOL_VERSION;
mv $TOOL_NAME-$TOOL_VERSION/* $TOOLS/$TOOL_NAME/$TOOL_VERSION;
rm -rf $TOOL_NAME-$TOOL_VERSION;
cd $TOOLS/$TOOL_NAME/$TOOL_VERSION/src;
make; \