From 13df59bfaf45d385fc7d745b31b9a174731da0ef Mon Sep 17 00:00:00 2001 From: phue Date: Tue, 12 Mar 2019 17:57:31 +0000 Subject: [PATCH] remove singularity support reasons: * the kernel running on the compute nodes does not support overlayfs und thus containers downloaded from public registries won't run because they lack the /lustre mountpoint * building containers manually using the Singularity file would work, however nf-core pipelines will stop providing these files in future releases --- conf/mendel.config | 2 +- docs/mendel.md | 18 +++--------------- 2 files changed, 4 insertions(+), 16 deletions(-) diff --git a/conf/mendel.config b/conf/mendel.config index 940a914..0715b42 100644 --- a/conf/mendel.config +++ b/conf/mendel.config @@ -11,7 +11,7 @@ manifest { } process { - beforeScript = {'module load Singularity; module load Miniconda3'} + beforeScript = 'module load Miniconda3/4.6.7' executor = 'pbspro' clusterOptions = { "-P $params.project" } } diff --git a/docs/mendel.md b/docs/mendel.md index 3f3db20..ae0ad4c 100644 --- a/docs/mendel.md +++ b/docs/mendel.md @@ -2,27 +2,15 @@ All nf-core pipelines have been successfully configured for use on the MENDEL CLUSTER at the Gregor Mendel Institute (GMI). -To use, run the pipeline with `-profile conda,mendel`. This will download and launch the [`mendel.config`](../conf/mendel.config) which has been pre-configured with a setup suitable for the MENDEL cluster. A Conda environment will be created automatically and software dependencies will be downloaded from ['bioconda'](https://bioconda.github.io/). +To use, run the pipeline with `-profile conda,mendel`. This will download and launch the [`mendel.config`](../conf/mendel.config) which has been pre-configured with a setup suitable for the MENDEL cluster. A Conda environment will be created automatically and software dependencies will be resolved via [bioconda](https://bioconda.github.io/). -Theoretically, using `-profile singularity,mendel` would download a docker image containing all of the required software, and convert it to a Singularity image before execution of the pipeline. However, there is a regression in the Singularity deployment on MENDEL which renders containers downloaded from public repositories unusable because they lack the /lustre mountpoint. - -If you want to run the pipeline containerized anyway you will have to build the image yourself (on a machine where you have root access) using the provided `Singularity` file in the pipeline repository: - -```bash -cd /path/to/pipeline-repository -echo 'mkdir /lustre > Singularity' -singularity build nf-core-methylseq-custom.simg Singularity -``` - -After you copied the container image to the cluster filesystem, make sure to pass the path to the image to the pipeline with `-with-singularity /path/to/nf-core-methylseq-custom.simg` - -Before running the pipeline you will need to load Nextflow and Conda using the environment module system on MENDEL. You can do this by issuing the commands below: +Before running the pipeline you will need to load Conda using the environment module system on MENDEL. You can do this by issuing the commands below: ```bash ## Load Nextflow and Conda environment modules module purge module load Nextflow -module load Miniconda3 # not needed if using Singularity +module load Miniconda/4.6.7 ``` >NB: You will need an account to use the HPC cluster in order to run the pipeline. If in doubt contact the HPC team.