snpeff_HIV.def

Bootstrap: docker
From: quay.io/biocontainers/snpeff:5.1--hdfd78af_2

%labels
    Author mdbdabrowska1
    Version 1.0

%help
    This container runs SnpEff 5.1 with addiitional support for custom HIV genome.

%setup
    mkdir /usr/local/share/HIV_GCA_003102975.1

%files
    /home/md1mbdx/Documents/snpeff_build/HIV_GCA_003102975.1/genes.gtf /usr/local/share/HIV_GCA_003102975.1/genes.gtf
    /home/md1mbdx/Documents/snpeff_build/HIV_GCA_003102975.1/cds.fa /usr/local/share/HIV_GCA_003102975.1/cds.fa
    /home/md1mbdx/Documents/snpeff_build/HIV_GCA_003102975.1/protein.fa /usr/local/share/HIV_GCA_003102975.1/protein.fa
    /home/md1mbdx/Documents/snpeff_build/HIV_GCA_003102975.1/sequences.fa /usr/local/share/HIV_GCA_003102975.1/sequences.fa

%post
    # Move HIV genome files
    mkdir /usr/local/share/snpeff-5.1-2/data
    mv /usr/local/share/HIV_GCA_003102975.1 /usr/local/share/snpeff-5.1-2/data/

    # Add HIV information into snpEff.config file
    echo "" >> /usr/local/share/snpeff-5.1-2/snpEff.config
    echo "# HIV Human immunodeficiency virus type 1 (HXB2)" >> /usr/local/share/snpeff-5.1-2/snpEff.config
    echo "HIV_GCA_003102975.1.genome : HIV" >> /usr/local/share/snpeff-5.1-2/snpEff.config

    # Build the HIV genome
    snpEff build -gtf22 -d HIV_GCA_003102975.1

    # Verify the build
    snpEff databases | grep "HIV"

    # Add metadata
    NOW=`date`
    echo "export NOW=\"${NOW}\"" >> $SINGULARITY_ENVIRONMENT

%runscript
    echo "Container was created $NOW"
    echo "Arguments received: $*"
    exec echo "$@"