From 865a71c47af71870c0dceb30d87e4b2d44a6bda1 Mon Sep 17 00:00:00 2001 From: Alan Hoyle Date: Wed, 13 Nov 2024 12:44:12 -0500 Subject: [PATCH 1/2] Corrected unc_lccc.md The details on how to run things have been corrected to reflect reality on our cluster. --- docs/unc_lccc.md | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/docs/unc_lccc.md b/docs/unc_lccc.md index 0287bf6d4..8ee6acb34 100644 --- a/docs/unc_lccc.md +++ b/docs/unc_lccc.md @@ -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 . -> NB: You will need an account to use the in order to run the pipelines. If in doubt contact . -> 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. From 931a20845d9004e9266f9100f71bf7d56faaa815 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 14 Nov 2024 10:19:29 +0000 Subject: [PATCH 2/2] [automated] Fix code linting --- docs/unc_lccc.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/unc_lccc.md b/docs/unc_lccc.md index 8ee6acb34..1ad9c0d99 100644 --- a/docs/unc_lccc.md +++ b/docs/unc_lccc.md @@ -6,7 +6,6 @@ To use, run the pipeline with `-profile unc_lccc` in the `nextflow run [...]` co ## Below are non-mandatory information -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. +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. > 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 . -