mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-24 00:59:55 +00:00
275 lines
11 KiB
Markdown
275 lines
11 KiB
Markdown
# nf-core/configs: UPPMAX Configuration
|
|
|
|
All nf-core pipelines have been successfully configured for use on the Swedish UPPMAX clusters.
|
|
|
|
## Getting help
|
|
|
|
We have a Slack channel dedicated to UPPMAX users on the nf-core Slack: [https://nfcore.slack.com/channels/uppmax](https://nfcore.slack.com/channels/uppmax)
|
|
|
|
## 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`).
|
|
|
|
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.
|
|
It will enable `Nextflow` to manage the pipeline jobs via the `Slurm` job scheduler.
|
|
Using this profile, `Docker` image(s) containing required software(s) will be downloaded, and converted to `Singularity` image(s) if needed before execution of the pipeline.
|
|
|
|
Recent version of `Nextflow` also support the environment variable `NXF_SINGULARITY_CACHEDIR` which can be used to supply images.
|
|
Images for some `nf-core` pipelines are available under `/sw/data/ToolBox/nf-core/` and those can be used by `NXF_SINGULARITY_CACHEDIR=/sw/data/ToolBox/nf-core/; export NXF_SINGULARITY_CACHEDIR`.
|
|
|
|
In addition to this config profile, you will also need to specify an UPPMAX project id.
|
|
You can do this with the `--project` flag (two hyphens) when launching `Nextflow`.
|
|
For example:
|
|
|
|
```bash
|
|
# Launch a nf-core pipeline with the uppmax profile for the project id snic2018-1-234
|
|
$ nextflow run nf-core/<PIPELINE> -profile uppmax --project snic2018-1-234 [...]
|
|
```
|
|
|
|
> NB: If you're not sure what your UPPMAX project ID is, try running `groups` or checking SUPR.
|
|
|
|
Just run `Nextflow` on a login node and it will handle everything else.
|
|
|
|
Remember to use `-bg` to launch `Nextflow` in the background, so that the pipeline doesn't exit if you leave your terminal session.
|
|
Alternatively, you can also launch `Nextflow` in a `screen` or a `tmux` session.
|
|
|
|
## Using AWS iGenomes references
|
|
|
|
A local copy of the `AWS iGenomes` resource has been made available on all UPPMAX clusters so you should be able to run the pipeline against any reference available in the `conf/igenomes.config`.
|
|
You can do this by simply using the `--genome <GENOME_ID>` parameter.
|
|
|
|
## Getting more memory
|
|
|
|
If your `nf-core` pipeline run is running out of memory, you can run on a fat node with more memory using the following `Nextflow` flags:
|
|
|
|
```bash
|
|
--clusterOptions "-C mem256GB -p node" --max_memory "256GB"
|
|
```
|
|
|
|
This raises the ceiling of available memory from the default of `128.GB` to `256.GB`.
|
|
`rackham` has nodes with 128GB, 256GB and 1TB memory available.
|
|
|
|
Note that each job will still start with the same request as normal, but restarted attempts with larger requests will be able to request greater amounts of memory.
|
|
|
|
All jobs will be submitted to fat nodes using this method, so it's only for use in extreme circumstances.
|
|
|
|
## Different UPPMAX clusters
|
|
|
|
The UPPMAX nf-core configuration profile uses the `hostname` of the active environment to automatically apply the following resource limits:
|
|
|
|
* `rackham`
|
|
* cpus available: 20 cpus
|
|
* memory available: 125 GB
|
|
* `bianca`
|
|
* cpus available: 16 cpus
|
|
* memory available: 109 GB
|
|
* `irma`
|
|
* cpus available: 16 cpus
|
|
* memory available: 250 GB
|
|
|
|
## Development config
|
|
|
|
If doing pipeline development work on UPPMAX, the `devel` profile allows for faster testing.
|
|
|
|
Applied after main UPPMAX config, it overwrites certain parts of the config and submits jobs to the `devcore` queue, which has much faster queue times.
|
|
|
|
All jobs are limited to 1 hour to be eligible for this queue and only one job allowed at a time.
|
|
It is not suitable for use with real data.
|
|
|
|
To use it, submit with `-profile uppmax,devel`.
|
|
|
|
## Running on bianca
|
|
|
|
> :warning: For more information, please follow the following guides:
|
|
>
|
|
> * [UPPMAX `bianca` user guide](http://uppmax.uu.se/support/user-guides/bianca-user-guide/).
|
|
> * [nf-core guide for running offline](https://nf-co.re/usage/offline)
|
|
> * [nf-core `tools` guide for downloading pipelines for offline use](https://nf-co.re/tools#downloading-pipelines-for-offline-use).
|
|
> * [UPPMAX `Singularity` guide](https://www.uppmax.uu.se/support-sv/user-guides/singularity-user-guide/).
|
|
|
|
For security reasons, there is no internet access on `bianca` so you can't download from or upload files to the cluster directly.
|
|
Before running a nf-core pipeline on `bianca` you will first have to download the pipeline and singularity images needed elsewhere and transfer them via the `wharf` area to your own `bianca` project.
|
|
|
|
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.
|
|
|
|
### 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
|
|
# Or stay in your terminal
|
|
|
|
# Download the nextflow-all bundle
|
|
$ wget https://github.com/nextflow-io/nextflow/releases/download/v<NEXTFLOW_VERSION>/nextflow-<NEXTFLOW_VERSION>-all
|
|
|
|
# Connect to the wharf area using sftp
|
|
$ sftp <USER>-<BIANCA_PROJECT>@bianca-sftp.uppmax.uu.se:<USER>-<BIANCA_PROJECT>
|
|
|
|
# Transfer nextflow to the wharf area
|
|
sftp> put nextflow-<NEXTFLOW_VERSION>-all .
|
|
|
|
# Exit sftp
|
|
$ exit
|
|
|
|
# Connect to bianca
|
|
$ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se
|
|
|
|
# Go to your project
|
|
$ cd /castor/project/proj_nobackup
|
|
|
|
# Make folder for Nextflow
|
|
$ mkdir tools
|
|
$ mkdir tools/nextflow
|
|
|
|
# Move Nextflow from the wharf area to its directory
|
|
$ mv /castor/project/proj_nobackup/wharf/<USER>/<USER>-<BIANCA_PROJECT>/nextflow-<NEXTFLOW_VERSION>-all /castor/project/proj_nobackup/tools/nextflow
|
|
|
|
# Establish permission
|
|
$ chmod a+x /castor/project/proj_nobackup/tools/nextflow/nextflow-<NEXTFLOW_VERSION>-all
|
|
|
|
# If you want other people to use it
|
|
# Be sure that your group has rights to the directory as well
|
|
$ chown -R .<BIANCA_PROJECT> /castor/project/proj_nobackup/tools/nextflow/nextflow-<NEXTFLOW_VERSION>-all
|
|
|
|
# Make a link to it
|
|
$ ln -s /castor/project/proj_nobackup/tools/nextflow/nextflow-<NEXTFLOW_VERSION>-all /castor/project/proj_nobackup/tools/nextflow/nextflow
|
|
|
|
# And every time you're launching Nextflow, don't forget to export the following ENV variables
|
|
# Or add them to your .bashrc file
|
|
$ export NXF_HOME=/castor/project/proj/nobackup/tools/nextflow/
|
|
$ export PATH=${NXF_HOME}:${PATH}
|
|
$ export NXF_TEMP=$SNIC_TMP
|
|
$ export NXF_LAUNCHER=$SNIC_TMP
|
|
$ export NXF_SINGULARITY_CACHEDIR=/castor/project/proj_nobackup/singularity-images
|
|
```
|
|
|
|
### 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
|
|
# Or stay in your terminal
|
|
|
|
# Install the latest pip version
|
|
$ pip3 install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev --user
|
|
```
|
|
|
|
### Download and transfer a nf-core pipeline
|
|
|
|
```bash
|
|
# Connect to rackham
|
|
$ ssh -X <USER>@rackham.uppmax.uu.se
|
|
# Or stay in your terminal
|
|
|
|
# Open an interactive session (if you are on rackham)
|
|
$ interactive <rackham_project>
|
|
|
|
# Download a pipeline with the singularity images
|
|
$ nf-core download <PIPELINE> -r <PIPELINE_VERSION> -s --compress none
|
|
|
|
# If necessary, extra singularity images can be download separately
|
|
# For example, if you downloaded nf-core/sarek, you will need extra images for annotation
|
|
# Here we download the nf-core/sarek GRCh38 specific images
|
|
$ singularity pull --name nfcore-sareksnpeff-2.7.GRCh38.img docker://nfcore/sareksnpeff:2.7.GRCh38
|
|
$ singularity pull --name nfcore-sarekvep-2.7.GRCh38.img docker://nfcore/sarekvep:2.7.GRCh38
|
|
|
|
# Which can then be moved into the nf-core/sarek download folder
|
|
$ mv *.img nf-core-sarek-2.7/singularity-images/.
|
|
|
|
# Connect to the wharf area using sftp
|
|
$ sftp <USER>-<BIANCA_PROJECT>@bianca-sftp.uppmax.uu.se:<USER>-<BIANCA_PROJECT>
|
|
|
|
# Transfer <PIPELINE> folder from rackham to the wharf area
|
|
sftp> put -r nf-core-<PIPELINE>-<PIPELINE_VERSION> .
|
|
|
|
# The archives will be in the wharf folder in your user home on your bianca project
|
|
|
|
# Connect to bianca
|
|
$ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se
|
|
|
|
# Go to your project
|
|
$ cd /castor/project/proj_nobackup
|
|
|
|
# Make and go into a nf-core directory (where you will store all nf-core pipelines')
|
|
$ mkdir nf-core
|
|
$ cd nf-core
|
|
|
|
# Move the folder from the wharf area to the project
|
|
$ cp /castor/project/proj_nobackup/wharf/<USER>/<USER>-<BIANCA_PROJECT>/nf-core-<PIPELINE>-<PIPELINE_VERSION> .
|
|
|
|
# If you want other people to use it,
|
|
# Be sure that your group has rights to the directory as well
|
|
$ chown -R .<BIANCA_PROJECT> nf-core-<PIPELINE>-<PIPELINE_VERSION>
|
|
|
|
# Make a symbolic link to the extracted repository
|
|
$ ln -s nf-core-<PIPELINE>-<PIPELINE_VERSION> nf-core-<PIPELINE>-default
|
|
```
|
|
|
|
The principle is to have every member of your project to be able to use the same `nf-core/<PIPELINE>` version at the same time.
|
|
So every member of the project who wants to use `nf-core/<PIPELINE>` will need to do:
|
|
|
|
```bash
|
|
# Connect to bianca
|
|
$ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se
|
|
|
|
# Go to your user directory
|
|
$ cd /home/<USER>
|
|
|
|
# Make a symbolic link to the default nf-core/<PIPELINE>
|
|
$ ln -s /castor/project/proj_nobackup/nf-core/nf-core-<PIPELINE>-default nf-core-<PIPELINE>
|
|
```
|
|
|
|
And then `nf-core/<PIPELINE>` can be used with:
|
|
|
|
```bash
|
|
# run <PIPELINE> on bianca
|
|
$ nextflow run ~/<PIPELINE> -profile uppmax --project <BIANCA_PROJECT> --genome <GENOME_ASSEMBLY> ...
|
|
```
|
|
|
|
## Update a pipeline
|
|
|
|
To update, repeat the same steps as for installing and update the link.
|
|
|
|
```bash
|
|
# Connect to bianca (Connect to rackham first if needed)
|
|
$ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se
|
|
|
|
# Go to the nf-core directory in your project
|
|
$ cd /castor/project/proj_nobackup/nf-core
|
|
|
|
# Remove link
|
|
$ unlink nf-core-<PIPELINE>-default
|
|
|
|
# Link to new nf-core/<PIPELINE> version
|
|
$ ln -s nf-core-<PIPELINE>-<PIPELINE_VERSION> nf-core-<PIPELINE>-default
|
|
```
|
|
|
|
You can for example keep a `nf-core-<PIPELINE>-default` version that you are sure is working, an make a link for a `nf-core-<PIPELINE>-testing` or `nf-core-<PIPELINE>-development`.
|