snakemake_tutorial.scif

%appinstall bwa
    # Dependencies of bwa
    apt-get -y install wget libbz2-dev zlib1g-dev

    # bwa itself
    wget https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2
    tar xvjf bwa-0.7.17.tar.bz2
    cp -r bwa-0.7.17/* lib 
    rm -r bwa-0.7.17
    rm bwa-0.7.17.tar.bz2
    cd lib
    make
    mv bwa ../bin
%apphelp bwa
    Burrows-Wheeler Aligner
%apprun bwa
    cd $SCIF_DATA
    exec bwa "$@"
%applabels bwa
    VERSION 0.7.17
%apptest bwa
    bwa "$@"

%appinstall samtools
    apt-get -y install wget libbz2-dev zlib1g-dev xz-utils liblzma-dev
    apt-get -y install libncurses5-dev
    # samtools
    wget https://github.com/samtools/samtools/releases/download/1.6/samtools-1.6.tar.bz2
    tar xvjf samtools-1.6.tar.bz2
    cd samtools-1.6
    ./configure --without-curses --prefix=$SCIF_APPROOT
    make
    make install
    cd ..
    rm -r samtools-1.6
    rm samtools-1.6.tar.bz2
    # bcftools
    wget https://github.com/samtools/bcftools/releases/download/1.6/bcftools-1.6.tar.bz2
    tar xvjf bcftools-1.6.tar.bz2
    cd bcftools-1.6
    ./configure --without-curses --prefix=$SCIF_APPROOT
    make
    make install
    cd ..
    rm -r bcftools-1.6
    rm bcftools-1.6.tar.bz2
%apphelp samtools
    This app provides Samtools suite, consisting of Samtools and BCFtools 
%apprun samtools
    cd $SCIF_DATA
    exec samtools "$@"
%applabels samtools
    VERSION 1.6
    URL http://www.htslib.org/
%apptest samtools
    exec samtools

%appinstall snakemake
%apphelp snakemake
    Run snakemake. The workflow is defined by a Snakefile that should be located in the $SCIF_APPDATA folder.
    This app does not provide snakemake itself, because it is already installed in the Singularity/Docker container.
    But it would be easy to install snakemake also in the app context.
%apprun snakemake
    cd $SCIF_APPDATA
    exec snakemake "$@"

%appinstall graphviz_create_dag
    apt-get -y install graphviz
%apphelp graphviz_create_dag
    This app creates a directed acyclic graph representation of a Snakemake workflow execution.
    The app takes three arguments: The directory of the Snakefile, the target file and the output filename.
%apprun graphviz_create_dag
    cd $1
    snakemake --dag $2 | dot -Tsvg > $SCIF_DATA/$3