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Merge pull request #426 from Aratz/master

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Update UPPMAX documentation
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Maxime U. Garcia 2022-10-10 16:39:58 +02:00 committed by GitHub
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@ -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/<VERSION>` 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 <USER>@{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 <USER>-<BIANCA_PROJECT>@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/<VERSION>`
```
```bash
# Connect to rackham
$ ssh -X <USER>@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 <USER>@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/<VERSION>`
```
```bash
# Connect to rackham
$ ssh -X <USER>@rackham.uppmax.uu.se
@ -254,7 +242,7 @@ And then `nf-core/<PIPELINE>` can be used with:
$ nextflow run ~/<PIPELINE> -profile uppmax --project <BIANCA_PROJECT> --genome <GENOME_ASSEMBLY> ...
```
## Update a pipeline
### Update a pipeline
To update, repeat the same steps as for installing and update the link.