Reproducing the build with Apptainer

The CRAN/CPU core of genoaligner builds and runs anywhere R does. When you want a reproducible, self-contained environment – pinned R, Rcpp and genoaligner, decoupled from whatever happens to be installed on the host – you can build it as an Apptainer (formerly Singularity) container with the recipe that ships in this repository.

The recipe lives at containers/genoaligner-r-compute.def. it is kept in the repo (and out of the CRAN tarball) so the exact construction recipe is version-controlled next to the code it pins.

What you get

A single .sif file holding R 4.4.1, Rcpp and genoaligner, plus the build recipe – so a colleague (or a cluster) can reproduce the environment without trusting your machine’s state.

The recipe

The file containers/genoaligner-r-compute.def:

Bootstrap: docker
From: rocker/r-ver:4.4.1

%files
    genoaligner_1.0.0.tar.gz /opt/

%post
    export DEBIAN_FRONTEND=noninteractive
    apt-get update
    apt-get install -y --no-install-recommends g++ make ca-certificates
    R -e 'install.packages("Rcpp", repos="https://cloud.r-project.org", quiet=TRUE)'
    R CMD INSTALL /opt/genoaligner_1.0.0.tar.gz
    R -e 'library(genoaligner); stopifnot(align("ACGT","ACGT",smax=8)$score==0); cat("BUILD_CORE_OK\n")'

%runscript
    exec Rscript "$@"