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2025-07-08Expose the batching systemMatthijs van der Wild
The queuing system was hard-coded to slurm. It may be, at times, convenient to be able to run workflows on the local node (or use a different queuing system altogether). The old behaviour is maintained by setting the batching system to slurm by default; the user can change the system by using --batch_system.
2025-04-09use a single assignment of possibly pre-set APPTAINER variablesMatthijs van der Wild
2025-04-07append to container PATH through APPTAINERENV_PREPEND_PATHMatthijs van der Wild
Apptainer v1.3.6-1.el9 doesn't appear to allow resetting the container path using APPTAINERENV_PATH. Using this variable works in v1.3.4, but it isn't clear where this change was introduced. APPTAINERENV_PREPEND_PATH is a safe alternative.
2025-04-07create vlbi-cwl_latest.sif symlinkMatthijs van der Wild
In some versions of toil the `:latest` tag appears to be automatically appended. This is a workaround for these versions.
2025-04-07place symlink in CWL_SINGULARITY_CACHE if it existsMatthijs van der Wild
2025-04-01make symlinking the container idempotentMatthijs van der Wild
2025-03-31place script directory at head of (PYTHON)PATHMatthijs van der Wild
2025-03-31ensure that scratch storage directory existsMatthijs van der Wild
2025-03-31ensure that $TMP_OUTDIR existsMatthijs van der Wild
2025-03-31update usage informationMatthijs van der Wild
2024-11-14Correct syntax in variable settingMatthijs van der Wild
2024-10-28Add missing closing parenthesisMatthijs van der Wild
2024-10-28Add option to specify a separate output directoryMatthijs van der Wild
2024-10-28Fix Markdown issueMatthijs van der Wild
2024-09-30Initialise repositoriesMatthijs van der Wild
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