diff --git a/docs/source/installation.rst b/docs/source/installation.rst index d19d7cd4824b6b6982b80f6e36fc4f949bfa13ae..9f838cfdb19d14c5e1b25e9776956d2f55926b7e 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -45,7 +45,7 @@ Once you have installed `cwltool`_ or `toil`_ locally on your system, LINC will You will find more details how to run **LINC** within an image on the page :doc:`how to run the pipeline<running>`. Manual installation --------------------------- +------------------- .. note:: Skip this section if you want to run **LINC** using software containers. diff --git a/docs/source/running.rst b/docs/source/running.rst index 3b850225c64f973e710616cc14d5e16ab9a225f1..bb7a0ac8eaca1ec6b0bdcdabbce3ca8c60395d8c 100644 --- a/docs/source/running.rst +++ b/docs/source/running.rst @@ -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. +Running **LINC** with a cached Singularity image +------------------------------------------------ + +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: + + $ singularity cache clean + Troubleshooting ---------------