scarHRD.def

Bootstrap: docker
From: quay.io/biocontainers/r-sequenza:3.0.0--r42h3342da4_5

%labels
    Application_name scarHRD commit c98f8bc with dependencies sequenza 3.0.0 and copynumber commit 2f54c08    
    Author Julia Wiggeshoff
    Author_email julia.wiggeshoff@uk-koeln.de
    Year 2026

%post

    echo 'options(repos="https://cloud.r-project.org")' >> /usr/local/lib/R/etc/Rprofile.site

    R -e 'if (!requireNamespace("remotes", quietly=TRUE)) install.packages("remotes")'

    R -e 'remotes::install_github("sztup/scarHRD@c98f8bc", dependencies=TRUE)'

    R -e 'remotes::install_github("aroneklund/copynumber@2f54c08", dependencies=TRUE)'

%environment
    export PATH="/usr/local/bin:$PATH"
    export R_LIBS="/usr/local/lib/R/site-library"

%runscript
    exec "$@"

%help
    This container includes:
    - Sequenza R package
    - scarHRD (R) pinned to c98f8bc
    - copynumber (R) pinned to 2f54c08
    - Python3