splicelauncher.recipe

# SpliceLauncher
# https://github.com/raphaelleman/SpliceLauncher
# Commit f2aa2efec29f173ad1dda4edd9c190e6e423cd3d

# base image: Ubuntu
Bootstrap: docker
From: ubuntu:16.04

# File Author / Maintainer
%labels
    MAINTAINER Frederic Lemoine <frederic.lemoine@pasteur.fr>

%environment
    export STAR_VERSION=2.6.0a
    export SAMTOOLS_VERSION=1.9
    export BEDTOOLS_VERSION=2.28.0

    export SPLICELAUNCHER_DIR=/usr/local/SpliceLauncher
    export PATH=${SPLICELAUNCHER_DIR}/scripts/:${SPLICELAUNCHER_DIR}:/usr/local/bin/:$PATH

    export LC_ALL="C"
    export LANG="C"
    export LANGUAGE="C"

    export CRANREPO="'http://cran.univ-paris1.fr/'"
    export RLIBPATH="'/usr/local/lib/R/site-library/'"

%files
    /stockage/stockage-01/gitlab/containers/splicelauncher/ressources/SpliceLauncher.zip /usr/local/
    
%post
    export STAR_VERSION=2.6.0a
    export SAMTOOLS_VERSION=1.9
    export BEDTOOLS_VERSION=2.28.0

    export SPLICELAUNCHER_DIR=/usr/local/SpliceLauncher
    export PATH=${SPLICELAUNCHER_DIR}/scripts/:${SPLICELAUNCHER_DIR}:/usr/local/bin/:$PATH

    export LC_ALL="C"
    export LANG="C"
    export LANGUAGE="C"

    export CRANREPO="'http://cloud.r-project.org/'"
    export RLIBPATH="'/usr/local/lib/R/site-library/'"
    
    SPLICELAUNCHER_PACKAGES="git"
    STAR_PACKAGES="gcc g++ make wget zlib1g-dev"
    SAMTOOLS_PACKAGES="wget gcc make libbz2-dev zlib1g-dev liblzma-dev libncurses5-dev bzip2"
    BEDTOOLS_PACKAGES="wget gcc g++ make zlib1g-dev"
    R_PACKAGES="libcairo2-dev libxt-dev"
    PACKAGES="zlib1g liblzma5 libncurses5 r-base python libcairo2 unzip bc"
    
    ## INSTALL ALL DEPS
    apt-get update --fix-missing
    apt-get install -y ${PACKAGES} ${SAMTOOLS_PACKAGES} ${STAR_PACKAGES} ${BEDTOOLS_PACKAGES} ${R_PACKAGES} ${SPLICELAUNCHER_PACKAGES}
    apt-get install -y r-base r-base-dev

    mkdir -p ${SPLICELAUNCHER_DIR}
    cd ${SPLICELAUNCHER_DIR}
    git clone http://github.com/raphaelleman/SpliceLauncher.git
    chmod -R +x ${SPLICELAUNCHER_DIR}/SpliceLauncher/*
    
    ## INSTALL STAR
    cd /usr/local
    wget --no-check-certificate "https://github.com/alexdobin/STAR/archive/${STAR_VERSION}.zip"
    unzip ${STAR_VERSION}.zip
    cd STAR-${STAR_VERSION}/source
    make STARstatic
    cp STAR /usr/local/bin
    cd /usr/local/

    ## INSTALL SAMTOOLS
    cd /usr/local/
    wget -O samtools.zip "https://github.com/samtools/samtools/archive/${SAMTOOLS_VERSION}.zip"
    unzip samtools.zip
    cd samtools-${SAMTOOLS_VERSION}
    wget -O htslib.zip "https://github.com/samtools/htslib/archive/${SAMTOOLS_VERSION}.zip"
    unzip htslib.zip
    cd htslib-${SAMTOOLS_VERSION}
    autoheader
    autoconf
    ./configure
    make
    make install
    cd ..
    autoheader
    autoconf -Wno-syntax
    ./configure
    make
    make install
    cd /usr/local

    ## INSTALL BEDTOOLS
    cd /usr/local/
    wget --no-check-certificate -O bedtools.zip "https://github.com/arq5x/bedtools2/archive/v${BEDTOOLS_VERSION}.zip"
    unzip bedtools.zip
    cd bedtools2-${BEDTOOLS_VERSION}
    make
    mv bin/* /usr/local/bin
    cd /usr/local

    ## INSTALL R LIBRARIES
    R -e "install.packages('WriteXLS',lib=$RLIBPATH,repo=$CRANREPO)"
    R -e "install.packages('Cairo',lib=$RLIBPATH,repo=$CRANREPO)"

    # ## COPY FILES INTO DOCKER
    # COPY . ${SPLICELAUNCHER_DIR}

    # ENTRYPOINT ${SPLICELAUNCHER_DIR}/SpliceLauncher/scripts/SpliceLauncher.r
    
%runscript
    ${SPLICELAUNCHER_DIR}/SpliceLauncher/SpliceLauncher.sh "$@"