From b20f28a3c9f3e4df21030b179a46ddb2fe151307 Mon Sep 17 00:00:00 2001 From: phue Date: Mon, 5 Sep 2022 11:25:33 +0200 Subject: [PATCH] biohpc_gen: load charliecloud from lrz software tree and remove conda fallback the biohpc_gen specific software tree is less maintained and outdated --- conf/biohpc_gen.config | 9 ++++----- docs/biohpc_gen.md | 6 ++---- 2 files changed, 6 insertions(+), 9 deletions(-) diff --git a/conf/biohpc_gen.config b/conf/biohpc_gen.config index e3f4069..694a25f 100755 --- a/conf/biohpc_gen.config +++ b/conf/biohpc_gen.config @@ -11,9 +11,8 @@ env { process { executor = 'slurm' - queue = { task.memory <= 1536.GB ? (task.time > 2.d || task.memory > 384.GB ? 'biohpc_gen_production' : 'biohpc_gen_normal') : 'biohpc_gen_highmem' } - beforeScript = 'module use /dss/dsslegfs02/pn73se/pn73se-dss-0000/spack/modules/x86_avx2/linux*' - module = 'charliecloud/0.22:miniconda3' + queue = { task.memory <= 1536.GB ? (task.time > 2.d || task.memory > 384.GB ? 'biohpc_gen_production' : 'biohpc_gen_normal') : 'biohpc_gen_highmem' } + module = 'charliecloud/0.25' } charliecloud { @@ -21,7 +20,7 @@ charliecloud { } params { - params.max_time = 14.d - params.max_cpus = 80 + params.max_time = 14.d + params.max_cpus = 80 params.max_memory = 3.TB } diff --git a/docs/biohpc_gen.md b/docs/biohpc_gen.md index c007cad..660e789 100644 --- a/docs/biohpc_gen.md +++ b/docs/biohpc_gen.md @@ -4,14 +4,12 @@ All nf-core pipelines have been successfully configured for use on the BioHPC Ge To use, run the pipeline with `-profile biohpc_gen`. This will download and launch the [`biohpc_gen.config`](../conf/biohpc_gen.config) which has been pre-configured with a setup suitable for the biohpc_gen cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Charliecloud container before execution of the pipeline. -Before running the pipeline you will need to load Nextflow and Charliecloud using the environment module system on biohpc_gen. You can do this by issuing the commands below: +Before running the pipeline you will need to load Nextflow and Charliecloud using the environment module system on a login node. You can do this by issuing the commands below: ```bash ## Load Nextflow and Charliecloud environment modules -module purge -module load nextflow charliecloud/0.22 +module load nextflow/21.04.3 charliecloud/0.25 ``` -> NB: Charliecloud support requires Nextflow version `21.03.0-edge` or later. > NB: You will need an account to use the LRZ Linux cluster as well as group access to the biohpc_gen cluster in order to run nf-core pipelines. > NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes.