@@ -173,6 +173,25 @@ You can restart a pipeline if using ``toil`` through adding the parameter ``--re
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@@ -173,6 +173,25 @@ You can restart a pipeline if using ``toil`` through adding the parameter ``--re
``toil``'s ``--restart`` option is only useful if a temporary error has occured, since it will always reuse the workflow and the data it originally has started with. If those needed to be changed (software update/corrupted or missing data), you will have to delete the ``jobStore`` and start a fresh run.
``toil``'s ``--restart`` option is only useful if a temporary error has occured, since it will always reuse the workflow and the data it originally has started with. If those needed to be changed (software update/corrupted or missing data), you will have to delete the ``jobStore`` and start a fresh run.
Running **LINC** with a cached Singularity image
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Typical reasons for which you would like to run **LINC** with a cached Singularity image:
* when running into a Docker pull limit.
* when compute nodes do not have an outbound connection to the internet or any similar firewall restrictions.
In such cases you need to set a special CWL environment variable to make use of it:
$ export CWL_SINGULARITY_CACHE=<cachedir>
$ export SINGULARITY_TMPDIR=<cachedir>/tmp
where ``<cachedir>`` is your chosen location of the Singularity image. When running **LINC**, the location of the ``<cachedir>`` should be visible from all compute nodes or machines you want to use. Once set simply restart your pipeline with ``--singularity`` and the image should be put into the right directory and be used for all steps.
Setting ``$SINGULARITY_TMPDIR`` is optional and avoids temporary mounting of the images in your ``/tmp``-directory. This is particularly helpful if your ``/tmp``-directory does not have much disk space.
If you need to update your **LINC** Singularity image, simply remove the ``astronrd_linc.sif`` file in your ``<cachedir>`` and clean the Singularity cache:
