mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-12-22 10:38:16 +00:00
33 lines
1.3 KiB
Markdown
33 lines
1.3 KiB
Markdown
# nf-core/configs: OIST Configuration
|
|
|
|
The nf-core pipelines [rnaseq](https://nf-co.re/rnaseq) and
|
|
[eager](https://nf-co.re/eager) have been successfully tested on the _Deigo_
|
|
cluster at the Okinawa Institute of Science and Technology Graduate University
|
|
([OIST](https://www.oist.jp)). We have no reason to expect that other
|
|
pipelines would not work.
|
|
|
|
To use, run the pipeline with `-profile oist`. This will download and launch
|
|
the [`oist.config`](../conf/oist.config) which has been pre-configured with a
|
|
setup suitable for _Deigo_. 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.
|
|
|
|
## Below are non-mandatory information e.g. on modules to load etc
|
|
|
|
Before running the pipeline you will need to load Nextflow and Singularity
|
|
using the environment module system on _Deigo_. You can do this by issuing the
|
|
commands below:
|
|
|
|
```bash
|
|
## Load the latest Nextflow and Singularity environment modules
|
|
ml purge
|
|
ml bioinfo-ugrp-modules
|
|
ml Other/Nextflow
|
|
```
|
|
|
|
> NB: You will need an account to use the _Deigo_ cluster in order to run the
|
|
> pipeline. If in doubt contact IT.
|
|
>
|
|
> NB: Nextflow will submit the jobs via the SLURM 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 IT.
|