From 7d59eabd91635879edab05ef9ec8f007b37e5bf4 Mon Sep 17 00:00:00 2001 From: qlr900 Date: Wed, 6 Jul 2022 09:52:06 +0200 Subject: [PATCH] simplify guideline --- docs/ku_sund_dangpu.md | 43 ++++++++---------------------------------- 1 file changed, 8 insertions(+), 35 deletions(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 9dafaa0..6121c87 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -1,58 +1,31 @@ # nf-core/configs: PROFILE Configuration -All nf-core pipelines have been successfully configured for use on the dangpu PROFILE CLUSTER at the +All nf-core pipelines have been successfully configured for use on the DANGPU at the Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and the Novo Nordisk Foundation Center for Protein Research (CPR) at the University of Copenhagen. -To use, run the pipeline with `-profile ku_sund_dangpu`. This will download and launch the [`ku_sund_dangpu.config`](../conf/ku_sund_dangpu.config) which has been pre-configured with a setup suitable for the PROFILE CLUSTER. +To use, run the pipeline with `-profile ku_sund_dangpu`. This will download and launch the [`ku_sund_dangpu.config`](../conf/ku_sund_dangpu.config) which has been pre-configured with a setup suitable for the DANGPU. ## Modules -Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on PROFILE CLUSTER. You can do this by issuing the commands below: +Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on DANGPU. You can do this by issuing the commands below: ```bash ## Load Nextflow and Singularity environment modules module purge module load openjdk/11.0.0 nextflow/22.04.3 singularity/3.8.0 -``` - -## How to use the nf-core pipelines on PROFILE CLUSTER - -###1. set up .bash_profile -Add memory restrictions to `.bash_profile`. Use `vim` text editor to edit `.bash_profile` file (or create one if it does not exist in your home directory: - -``` -vi ~/.bash_profile -``` - -paste the following text within the file: -``` -# personalising the profile: change the value of the variable $abc123 to your own user id -abc123=def456 - -# In some cases, the Nextflow Java virtual machines can start to request a large amount of memory. We recommend adding the following line to your environment to limit this export NXF_OPTS='-Xms1g -Xmx4g' - -# Don't fill up your home directory with cache files -export NXF_HOME=/projects/dan1/people/${abc123}/cache/nxf-home -export NXF_TEMP=${SNIC_TMP:-$HOME/glob/nxftmp} - -# Nextflow singularity image cachedir export -NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${abc123}/cache/singularity-images +export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home +export NXF_TEMP=/scratch/tmp +NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images ``` -then save the changes and exit the editor. Now you need to activate the `.bash_profile` by logging out and in again to PROFILE CLUSTER or by typing: -``` -source .bash_profile -``` - -The `$HOME` directory at dangpu has restricted space and should not be used to store cache files. Create those designated cache spaces for nextflow and singularity outside your `$HOME`: +create nextflow directories if they dont exist: ``` mkdir $NXF_SINGULARITY_CACHEDIR mkdir $NXF_HOME ``` -### 3. choose a nf-core pipeline and test it with your preferred settings +finally download and test the pipeline of choice using the `-profile ku_sund_dangpu` ``` nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu ``` -