diff --git a/docs/uppmax.md b/docs/uppmax.md index 891762a..dd664fb 100644 --- a/docs/uppmax.md +++ b/docs/uppmax.md @@ -8,7 +8,16 @@ We have a Slack channel dedicated to UPPMAX users on the nf-core Slack: [https:/ ## Using the UPPMAX config profile -Before running the pipeline you will need to either install `Nextflow` or load it using the environment module system (this can be done with e.g. `module load bioinfo-tools Nextflow/` where `VERSION` is e.g. `20.10`). +The recommended way to activate `Nextflow`, `nf-core`, and any pipeline +available in `nf-core` on UPPMAX is to use the [module system](https://www.uppmax.uu.se/resources/software/module-system/): + +```bash +# Log in to the desired cluster +ssh @{rackham,miarka,bianca}.uppmax.uu.se + +# Activate the modules, you can also choose to use a specific version with e.g. `Nextflow/21.10`. +module load bioinfo-tools Nextflow nf-core nf-core-pipelines +``` To use, run the pipeline with `-profile uppmax` (one hyphen). This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers. @@ -94,21 +103,13 @@ Before running a nf-core pipeline on `bianca` you will first have to download th In this guide, we use `rackham` to download and transfer files to the `wharf` area, but it can also be done on your own computer. If you use `rackham` to download the pipeline and the singularity containers, we recommend using an interactive session (cf [interactive guide](https://www.uppmax.uu.se/support/faq/running-jobs-faq/how-can-i-run-interactively-on-a-compute-node/)), which is what we do in the following guide. +It is recommended to activate `Nextflow`, `nf-core` and your `nf-core` +pipeline through the module system (see **Using the UPPMAX config profile** +above). In case you need a specific version of any of these tools you can +follow the guide below. + ### Download and install Nextflow -You can use the `Nextflow` UPPMAX provided `module`, but if necessary, you can also download a more recent version. - -```bash -# Connect to bianca -$ ssh -A -@bianca.uppmax.uu.se - -# See the available versions for the module -module spider Nextflow - -# Load a specific version of the Nextflow module -module load bioinfo-tools Nextflow/` -``` - ```bash # Connect to rackham $ ssh -X @rackham.uppmax.uu.se @@ -160,19 +161,6 @@ $ export NXF_SINGULARITY_CACHEDIR=/castor/project/proj_nobackup/singularity-imag ### Install nf-core tools -You can use the `nf-core` UPPMAX provided `module`, but if necessary, you can also download a more recent version. - -```bash -# Connect to rackham -$ ssh -X @rackham.uppmax.uu.se - -# See the available versions for the module -module spider nf-core - -# Load a specific version of the nf-core module -module load bioinfo-tools nf-core/` -``` - ```bash # Connect to rackham $ ssh -X @rackham.uppmax.uu.se @@ -254,7 +242,7 @@ And then `nf-core/` can be used with: $ nextflow run ~/ -profile uppmax --project --genome ... ``` -## Update a pipeline +### Update a pipeline To update, repeat the same steps as for installing and update the link.