---
title: "Reproducing the build with Apptainer"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Reproducing the build with Apptainer}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(eval = FALSE, collapse = TRUE, comment = "#>")
```

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](https://apptainer.org) (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`:

```{sh, eval=FALSE}
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_edit("ACGT","ACGT",smax=8)$score==0); cat("BUILD_CORE_OK\n")'

%runscript
    exec Rscript "$@"
```