From 26183d988339b03d224af7037e1d58aeea3a355b Mon Sep 17 00:00:00 2001 From: ameynert Date: Fri, 23 Jul 2021 09:35:15 +0100 Subject: [PATCH] Updated eddie documentation for singularity cache directory --- docs/eddie.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/docs/eddie.md b/docs/eddie.md index 485e20a..e35f65a 100644 --- a/docs/eddie.md +++ b/docs/eddie.md @@ -35,16 +35,17 @@ This config enables Nextflow to manage the pipeline jobs via the SGE job schedul ## Singularity set-up -Load Singularity from the module system and, if you have access to `/exports/igmm/eddie/BioinformaticsResources`, set the Singularity cache directory to the BioinformaticsResources path below. If some containers for your pipeline run are not present, please contact the [IGC Data Manager](data.manager@igc.ed.ac.uk) to have them added. You can add these lines to the file `$HOME/.bashrc`, or you can run these commands before you run an nf-core pipeline. - -If you do not have access to `/exports/igmm/eddie/BioinformaticsResources`, set the Singularity cache directory to somewhere sensible that is not in your `$HOME` area (which has limited space). It will take time to download all the Singularity containers, but you can use this again. +Load Singularity from the module system. ```bash module load singularity -export NXF_SINGULARITY_CACHEDIR="/exports/igmm/eddie/BioinformaticsResources/nf-core/singularity-images" ``` -Singularity will create a directory `.singularity` in your `$HOME` directory on eddie. Space on `$HOME` is very limited, so it is a good idea to create a directory somewhere else with more room and link the locations. +The eddie profile is set to use `/exports/igmm/eddie/BioinformaticsResources/nf-core/singularity-images` as the Singularity cache directory. If some containers for your pipeline run are not present, please contact the [IGC Data Manager](data.manager@igc.ed.ac.uk) to have them added. You can add these lines to the file `$HOME/.bashrc`, or you can run these commands before you run an nf-core pipeline. + +If you do not have access to `/exports/igmm/eddie/BioinformaticsResources`, set the Singularity cache directory to somewhere sensible that is not in your `$HOME` area (which has limited space). It will take time to download all the Singularity containers, but you can use this again. + +Singularity will by default create a directory `.singularity` in your `$HOME` directory on eddie. Space on `$HOME` is very limited, so it is a good idea to create a directory somewhere else with more room and link the locations. ```bash cd $HOME