René's URL Explorer Experiment

{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"Built-in templates: Add support for running 'Rscript' in a Linux container, etc.","articleBody":"# Wish\nAdd support for launching `Rscript` via a Linux container, e.g.\n\n```sh\n## Call batchtools inside container\nmodule load apptainer/latest\nexport APPTAINER_BINDPATH=\"/run/munge,/var/run/munge,/etc/slurm,/var/spool/slurm/slurmd/conf-cache/slurm.conf,$APPTAINER_BINDPATH\"\n\napptainer exec /modules/admin-resources/ood-dev/unity-r_4.4.0.sif Rscript --no-restore --quiet --no-save -e 'batchtools::doJobCollection(\"\u003c%= uri %\u003e\")'\n```\n\nSource: https://github.com/mlr-org/batchtools/pull/314#issuecomment-3285931770\n\n\n# Idea\n\n* [x] Add support for specifying how `Rscript` is launched, e.g. \n\n```r\nplan(batchtools_slurm, resources = list(rscript = c(\"/modules/admin-resources/ood-dev/unity-r_4.4.0.sif\", '--bind=\"/run/munge,/var/run/munge,/etc/slurm,/var/spool/slurm/slurmd/conf-cache/slurm.conf,$APPTAINER_BINDPATH\"', \"Rscript\", \"--no-restore\", \"--quiet\", \"--no-save\"))\n```\n\nThis would then become the following in the rendered job script:\n\n```r\n/modules/admin-resources/ood-dev/unity-r_4.4.0.sif --bind=\"/run/munge,/var/run/munge,/etc/slurm,/var/spool/slurm/slurmd/conf-cache/slurm.conf,$APPTAINER_BINDPATH\" Rscript -e 'batchtools::doJobCollection(\"\u003c%= uri %\u003e\")'\n```\n\n* [x] Add support for specifying `Rscript` options when launching the **batchtools** job (inspired by https://parallelly.futureverse.org/reference/makeClusterPSOCK.html), e.g. \n\n```r\nplan(batchtools_slurm, resources = list(rscript_args = c(\"--no-restore\", \"--quiet\", \"--no-save\"))\n```\n\nThis would then become the following in the rendered job script:\n\n```r\nRscript --no-restore --quiet --no-save -e 'batchtools::doJobCollection(\"\u003c%= uri %\u003e\")'\n```\n\n* [x] Add support for setting environment variables, e.g.\n\n```r\nplan(batchtools_slurm, resources = list(rscript = c(\"/modules/admin-resources/ood-dev/unity-r_4.4.0.sif\", \"Rscript\"), envs = c(APPTAINER_BINDPATH = \"/run/munge,/var/run/munge,/etc/slurm,/var/spool/slurm/slurmd/conf-cache/slurm.conf,$APPTAINER_BINDPATH\"))\n```\n\n```r\nexport APPTAINER_BINDPATH=\"/run/munge,/var/run/munge,/etc/slurm,/var/spool/slurm/slurmd/conf-cache/slurm.conf,$APPTAINER_BINDPATH\"\n\n/modules/admin-resources/ood-dev/unity-r_4.4.0.sif Rscript -e 'batchtools::doJobCollection(\"\u003c%= uri %\u003e\")'\n```\n\n","author":{"url":"https://github.com/HenrikBengtsson","@type":"Person","name":"HenrikBengtsson"},"datePublished":"2025-09-12T16:58:34.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":1},"url":"https://github.com/99/future.batchtools/issues/99"}