-
Notifications
You must be signed in to change notification settings - Fork 277
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
The details on how to run things have been corrected to reflect reality on our cluster.
- Loading branch information
Showing
1 changed file
with
5 additions
and
12 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,19 +1,12 @@ | ||
# nf-core/configs: PROFILE Configuration | ||
|
||
All nf-core pipelines have been successfully configured for use on the Lineberger Bioinformatics Group cluster at the University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center. | ||
nf-core pipelines have been successfully configured for use on the Lineberger Bioinformatics Group cluster at the University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center. | ||
|
||
To use, run the pipeline with `-profile unc_lccc`. This will download and launch the [`unc_lccc.config`](../conf/unc_lccc.config) which has been pre-configured with a setup suitable for the LBG cluster. Using this profile, docker images containing all of the required software will be downloaded, and converted to a Singularity/Apptainer image before execution of the pipeline. | ||
To use, run the pipeline with `-profile unc_lccc` in the `nextflow run [...]` command. This will download and launch the [`unc_lccc.config`](../conf/unc_lccc.config) which has been pre-configured with a setup suitable for the LBG cluster. Using this profile, Docker images containing all of the required software will be downloaded, and converted to a Apptainer/Singularity image during execution of the pipeline. | ||
|
||
## Below are non-mandatory information e.g. on modules to load etc | ||
## Below are non-mandatory information | ||
|
||
Before running pipelines you will need to login to a compute node and install nextflow https://www.nextflow.io/. You can do this by issuing the commands below: | ||
Before running pipelines you should login to a compute node and install `nextflow` into your home directory. Directions at the following link: https://www.nextflow.io/. There is a copy of the `nextflow` executable in our default setup, but it tends to lag behind the released versions, so may or may not work with a given workflow. | ||
|
||
```bash | ||
## install Nextflow | ||
module purge | ||
module load Nextflow/0.32.0 | ||
module load Singularity/2.6.0 | ||
``` | ||
> NB: You will need an account to use the in order to run the pipelines and the `nextflow` commands will need to run on compute nodes, not a login node. If in doubt contact <[email protected]>. | ||
> NB: You will need an account to use the in order to run the pipelines. If in doubt contact <[email protected]>. | ||
> NB: Nextflow will need to submit the jobs via the job 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. |