From 7c1c4c7fa441f1ef3c3eb124cab50134f5e7ca1e Mon Sep 17 00:00:00 2001 From: rbpisupati Date: Wed, 2 Feb 2022 22:42:13 +0100 Subject: [PATCH] changes to cbe module loading --- conf/cbe.config | 4 ++-- docs/cbe.md | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/cbe.config b/conf/cbe.config index 0a5763f..e8d7bc0 100755 --- a/conf/cbe.config +++ b/conf/cbe.config @@ -9,11 +9,11 @@ process { executor = 'slurm' queue = { task.memory <= 170.GB ? 'c' : 'm' } clusterOptions = { task.time <= 8.h ? '--qos short': task.time <= 48.h ? '--qos medium' : '--qos long' } - module = 'anaconda3/2019.10' + module = ['build-env/.f2021', 'build-env/f2021', 'anaconda3/2021.11'] } singularity { - enabled = true + // enabled = true cacheDir = '/resources/containers' } diff --git a/docs/cbe.md b/docs/cbe.md index aa6c60d..217e1f2 100644 --- a/docs/cbe.md +++ b/docs/cbe.md @@ -2,7 +2,7 @@ All nf-core pipelines have been successfully configured for use on the CLIP BATCH ENVIRONMENT (CBE) cluster at the Vienna BioCenter (VBC). -To use, run the pipeline with `-profile cbe`. This will download and launch the [`cbe.config`](../conf/cbe.config) which has been pre-configured with a setup suitable for the CBE cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. +To use, run the pipeline with `-profile cbe`. This will download and launch the [`cbe.config`](../conf/cbe.config) which has been pre-configured with a setup suitable for the CBE cluster. This profile sets needed slurm environment. Additionally you need to add `sigularity`, `docker` or `conda` to the profile to be able to run the pipeline. If `-profile cbe,singularity` is given, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. Before running the pipeline you will need to load Nextflow using the environment module system on CBE. You can do this by issuing the commands below: