snpEff.recipe

Bootstrap:docker
From:alpine:3.17.1

%environment
    SNPEFF_VERSION=v4.3t

%labels
    Maintainer	gpvoshol@gmail.com

%post
    apk --update add wget curl build-base git ca-certificates openjdk8-jre unzip bash python3 py3-pip

    # Temp dir for downloading and building stuff
    TMPDIR=/build

    mkdir $TMPDIR
    cd $TMPDIR

    # the installation directory of snpEff
    INSTALLDIR=/usr/local/lib
    BINDIR=/usr/local/bin

    # Download snpEff version 5.1d
    #wget -P $TMPDIR https://snpeff.blob.core.windows.net/versions/snpEff_v5_1d_core.zip
    wget -P $TMPDIR http://sourceforge.net/projects/snpeff/files/snpEff_v4_3t_core.zip

    # Unzip snpEff archive
    ls $TMPDIR | xargs -i unzip "$TMPDIR/{}" -d $INSTALLDIR

    echo "#!/bin/sh" > $BINDIR/snpEff

    echo "java -jar $INSTALLDIR/snpEff/snpEff.jar \$*" >> $BINDIR/snpEff

    cp -r $INSTALLDIR/snpEff/* $BINDIR/

    chmod +x $BINDIR/snpEff

    # snpEff needs a data directory to which it can write
    # (Downloading reference genomes for example)
    mkdir $INSTALLDIR/snpEff/data
    chmod 777 -R $INSTALLDIR/snpEff/data

    # Remove tmp snpEff directory
    rm -rf $TMPDIR

    #Clean up
    rm -rf /var/cache/apk/*

    cd /
    rm -rf /build

    pip3 install git+https://github.com/SergeWielhouwer/SnpEffWrapper.git --use-pep517