From 6fc65b54a28c2213aa702263501c069339adce45 Mon Sep 17 00:00:00 2001 From: phue Date: Wed, 27 Feb 2019 22:26:31 +0000 Subject: [PATCH] add mendel.md --- docs/mendel.md | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 docs/mendel.md diff --git a/docs/mendel.md b/docs/mendel.md new file mode 100644 index 0000000..3f3db20 --- /dev/null +++ b/docs/mendel.md @@ -0,0 +1,30 @@ +# nf-core/configs: MENDEL Configuration + +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/). + +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: + +```bash +## Load Nextflow and Conda environment modules +module purge +module load Nextflow +module load Miniconda3 # not needed if using Singularity +``` + +>NB: You will need an account to use the HPC cluster in order to run the pipeline. If in doubt contact the HPC team. + +>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. If in doubt contact the HPC team.