diff --git a/docs/processing/environment.md b/docs/processing/environment.md index eab4f4a9..51718ff3 100644 --- a/docs/processing/environment.md +++ b/docs/processing/environment.md @@ -172,6 +172,35 @@ To fetch the dataset from the RIA store, you will need your SSH key be added to git annex initremote --private --sameas=ria-storage curnagl-storage type=external externaltype=ora encryption=none url="ria+file://{{ secrets.data.curnagl_ria_store | default('') }}" ``` +In addition to reconfiguring the RIA store, we should execute `datalad get` within a compute node: + +- [ ] Create a *sbatch* job prescription script called `datalad-get.sbatch`: + ```Bash + #!/bin/bash -l + + #SBATCH --account {{ secrets.data.curnagl_account | default('_') }} + + #SBATCH --chdir {{ secrets.data.curnagl_workdir | default('') }}/data/hcph-dataset + #SBATCH --job-name datalad_get + #SBATCH --partition cpu + #SBATCH --cpus-per-task 12 + #SBATCH --mem 10G + #SBATCH --time 05:00:00 + #SBATCH --export NONE + + #SBATCH --mail-type ALL + #SBATCH --mail-user + #SBATCH --output /users/%u/logs/%x-%A-%a.out + #SBATCH --error /users/%u/logs/%x-%A-%a.err + + + micromamba run -n fmriprep datalad get -J${SLURM_CPUS_PER_TASK} . + ``` +- [ ] Submit the job: + ```Bash + sbatch datalad-get.sbatch + ``` + ## Registering containers We use *DataLad containers-run* to execute software while keeping track of provenance.