singularity-recipes/scarHRD_new.def at main · juliawiggeshoff/singularity-recipes · GitHub

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Bootstrap: docker
From: quay.io/biocontainers/samtools:1.22.1--h96c455f_0
Stage: samtools

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

%labels
    Application_name scarHRD commit c98f8bc with sequenza 3.0.0, samtools 1.22.1, tabix, and copynumber commit 2f54c08
    Author Julia Wiggeshoff
    Author_email julia.wiggeshoff@uk-koeln.de
    Year 2026

%files from samtools
    /usr/local/bin/samtools   /usr/local/bin/samtools
    /usr/local/bin/tabix      /usr/local/bin/tabix
    /usr/local/lib/libhts.so.3      /usr/local/lib/libhts.so.3
    /usr/local/lib/libtinfow.so.6   /usr/local/lib/libtinfow.so.6
    /usr/local/lib/libncursesw.so.6 /usr/local/lib/libncursesw.so.6
    /usr/local/lib/libz.so.1        /usr/local/lib/libz.so.1
    /usr/local/lib/libdeflate.so.0  /usr/local/lib/libdeflate.so.0
    /usr/local/lib/liblzma.so.5     /usr/local/lib/liblzma.so.5
    /usr/local/lib/libbz2.so.1.0    /usr/local/lib/libbz2.so.1.0

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

%runscript
    echo "This container provides Sequenza (Python + R utils), samtools, tabix, scarHRD, and copynumber"
    exec "$@"

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