mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-23 08:49:54 +00:00
51 lines
2.3 KiB
Markdown
51 lines
2.3 KiB
Markdown
# nf-core/configs: Myriad Configuration
|
|
|
|
All nf-core pipelines have been successfully configured for use on UCL's myriad cluster [University College London](https://www.rc.ucl.ac.uk/docs/Clusters/Myriad/).
|
|
|
|
To use, run the pipeline with `-profile ucl_myriad`. This will download and launch the [`ucl_myriad.config`](../conf/ucl_myriad.config) which has been pre-configured with a setup suitable for the myriad cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
|
|
|
|
## Using Nextflow on Myriad
|
|
|
|
Before running the pipeline you will need to install and configure Nextflow and Singularity.
|
|
|
|
### Singularity
|
|
|
|
This can be done with the following commands:
|
|
|
|
```bash
|
|
## Load Singularity environment modules - these commands can be placed in your ~/.bashrc also
|
|
module add java/openjdk-11/11.0.1
|
|
module add singularity-env/1.0.0
|
|
```
|
|
|
|
Then set the correct configuration of the cache directories, where <YOUR_ID> is replaced with you credentials which you can find by entering `whoami` into the terminal once you are logged into myriad. Once you have added your credentials save these lines into your .bashrc file in the base directory (e.g. /home/<YOUR_ID>/.bashrc):
|
|
|
|
```bash
|
|
# Set all the Singularity cache dirs to Scratch
|
|
export SINGULARITY_CACHEDIR=/home/<YOUR_ID>/Scratch/.singularity/
|
|
export SINGULARITY_TMPDIR=/home/<YOUR_ID>/Scratch/.singularity/tmp
|
|
export SINGULARITY_LOCALCACHEDIR=/home/<YOUR_ID>/Scratch/.singularity/localcache
|
|
export SINGULARITY_PULLFOLDER=/home/<YOUR_ID>/Scratch/.singularity/pull
|
|
|
|
# Bind your Scratch directory so it is accessible from inside the container
|
|
export SINGULARITY_BINDPATH=/scratch/scratch/<YOUR_ID>
|
|
```
|
|
|
|
### Nextflow
|
|
|
|
Download the latest release of nextflow. Warning: the self-update line should update to the latest version, but sometimes not, so please check which is the latest release (https://github.com/nextflow-io/nextflow/releases), you can then manually set this by entering (`NXF_VER=XX.XX.X`).
|
|
|
|
```bash
|
|
## Download Nextflow-all
|
|
curl -s https://get.nextflow.io | bash
|
|
NXF_VER=22.10.0
|
|
nextflow -self-update
|
|
chmod a+x nextflow
|
|
mv nextflow ~/bin/nextflow
|
|
```
|
|
|
|
Then make sure that your bin PATH is executable, by placing the following line in your .bashrc:
|
|
|
|
```bash
|
|
export PATH=$PATH:/home/<YOUR_ID>/bin
|
|
```
|