From b240142cc327020832cdaafe1ccba6b5fd0b642c Mon Sep 17 00:00:00 2001 From: theoportlock Date: Wed, 8 Sep 2021 14:33:39 +0200 Subject: [PATCH] Adds rosalind configuration --- .github/workflows/main.yml | 1 + README.md | 1 + conf/rosalind.config | 28 ++++++++++++++++++++++++++++ docs/cambridge.md | 2 +- docs/rosalind.md | 23 +++++++++++++++++++++++ nfcore_custom.config | 1 + 6 files changed, 55 insertions(+), 1 deletion(-) create mode 100644 conf/rosalind.config create mode 100644 docs/rosalind.md diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index c5e6a57..f1f658d 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -52,6 +52,7 @@ jobs: - 'pasteur' - 'phoenix' - 'prince' + - 'rosalind' - 'sanger' - 'seg_globe' - 'shh' diff --git a/README.md b/README.md index 29fbce2..dc50e8a 100644 --- a/README.md +++ b/README.md @@ -125,6 +125,7 @@ Currently documentation is available for the following systems: * [PASTEUR](docs/pasteur.md) * [PHOENIX](docs/phoenix.md) * [PRINCE](docs/prince.md) +* [ROSALIND](docs/rosalind.md) * [SANGER](docs/sanger.md) * [SEG_GLOBE](docs/seg_globe.md) * [SHH](docs/shh.md) diff --git a/conf/rosalind.config b/conf/rosalind.config new file mode 100644 index 0000000..bb967c3 --- /dev/null +++ b/conf/rosalind.config @@ -0,0 +1,28 @@ +params { + config_profile_description = 'Kings College London Rosalind HPC' + config_profile_contact = 'Theo Portlock' + config_profile_url = 'https://www.rosalind.kcl.ac.uk/' +} + +singularity { + enabled = true + autoMounts = true + docker.enabled = false +} + +params { + max_memory = 64.GB + max_cpus = 16 + max_time = 24.h + partition = 'shared' +} + +process { + executor = 'slurm' + maxRetries = 3 + clusterOptions = { "--partition=$params.partition ${params.clusterOptions ?: ''}" } +} + +executor { + submitRateLimit = '1 sec' +} diff --git a/docs/cambridge.md b/docs/cambridge.md index ce833d7..4f18088 100644 --- a/docs/cambridge.md +++ b/docs/cambridge.md @@ -1,7 +1,7 @@ # nf-core/configs: Cambridge HPC Configuration All nf-core pipelines have been successfully configured for use on the Cambridge HPC cluster at the [The University of Cambridge](https://www.cam.ac.uk/). -To use, run the pipeline with `-profile cambridge`. This will download and launch the [`cambridge.config`](../conf/cambridge.config) whichhas been pre-configured +To use, run the pipeline with `-profile cambridge`. This will download and launch the [`cambridge.config`](../conf/cambridge.config) which has been pre-configured with a setup suitable for the Cambridge HPC cluster. Using this profile, either a docker image containing all of the required software will be downloaded, and converted to a Singularity image or a Singularity image downloaded directly before execution of the pipeline. diff --git a/docs/rosalind.md b/docs/rosalind.md new file mode 100644 index 0000000..6828c87 --- /dev/null +++ b/docs/rosalind.md @@ -0,0 +1,23 @@ +# nf-core/configs: Rosalind Configuration + +All nf-core pipelines have been successfully configured for use on the Rosalind CLuster at [Kings College London](https://rosalind.kcl.ac.uk/). +To use, run the pipeline with `-profile rosalind`. This will download and launch the [`rosalind.config`](../conf/rosalind.config) which has been pre-configured with a setup suitable for the rosalind 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 Rosalind + +Before running the pipeline you will need to configure Nextflow and Singularity. There is no Nextflow module on Rosalind at this time. This can be done with the following commands: + +```bash +## Load Singularity environment modules - these commands can be placed in your ~/.bashrc also +module load apps/openjdk +module load apps/singularity + +## Download Nextflow-all +wget https://github.com/nextflow-io/nextflow/releases/download/v21.04.3/nextflow-21.04.3-all +chmod a+x nextflow-21.04.3-all +mv nextflow-21.04.3-all ~/bin/nextflow +``` + +## Additional information + +The default shared partition resource limits are defined as ten percent of the total available to the cluster at any one point in time. The limitations defined by this configuration are conservative and are projected to be increased as greater computational resources are introduced in the near future. diff --git a/nfcore_custom.config b/nfcore_custom.config index 74d25b9..19a2bb1 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -46,6 +46,7 @@ profiles { pasteur { includeConfig "${params.custom_config_base}/conf/pasteur.config" } phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } prince { includeConfig "${params.custom_config_base}/conf/prince.config" } + rosalind { includeConfig "${params.custom_config_base}/conf/rosalind.config" } sanger { includeConfig "${params.custom_config_base}/conf/sanger.config"} seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"} shh { includeConfig "${params.custom_config_base}/conf/shh.config" }