From 8b3951b244e8a529ff41cd5bef249d59ca624beb Mon Sep 17 00:00:00 2001 From: Anthony Underwood Date: Thu, 22 Apr 2021 16:00:37 +0100 Subject: [PATCH 1/4] Create cambridge.config --- conf/cambridge.config | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 conf/cambridge.config diff --git a/conf/cambridge.config b/conf/cambridge.config new file mode 100644 index 0000000..3c970b7 --- /dev/null +++ b/conf/cambridge.config @@ -0,0 +1,18 @@ +params { + config_profile_description = 'Cambridge HPC cluster profile.' + config_profile_contact = 'Andries van Tonder (ajv37@cam.ac.uk)' + config_profile_url = "https://docs.hpc.cam.ac.uk/hpc" +} +singularity { + enabled = true + autoMounts = true +} +process { + executor = 'slurm' + clusterOptions = '-p cclake' +} +params { + max_memory = 192.GB + max_cpus = 56 + max_time = 12.h +} From 29dcc160e388bb7d961e67255045fe2b4b27a082 Mon Sep 17 00:00:00 2001 From: Anthony Underwood Date: Thu, 22 Apr 2021 16:04:29 +0100 Subject: [PATCH 2/4] Create cambridge.md --- docs/cambridge.md | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 docs/cambridge.md diff --git a/docs/cambridge.md b/docs/cambridge.md new file mode 100644 index 0000000..3f6373e --- /dev/null +++ b/docs/cambridge.md @@ -0,0 +1,17 @@ +# 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 +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. + +The latest version of Nextflow is not installed by default on the Cambridge HPC cluster. You will need to install it into a directory you have write access to. +Follow these instructions from the Nextflow documentation. + +- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#) + +All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline +has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway. + +> NB: You will need an account to use the Cambridge HPC cluster in order to run the pipeline. If in doubt contact IT. +> NB: Nextflow will need to submit the jobs via SLURM to the Cambridge 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 982d1a8f2a297b2e0662828ae83b87fc2588a356 Mon Sep 17 00:00:00 2001 From: Anthony Underwood Date: Thu, 22 Apr 2021 16:41:05 +0100 Subject: [PATCH 3/4] Fix markdown linting --- docs/cambridge.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/cambridge.md b/docs/cambridge.md index 3f6373e..ce833d7 100644 --- a/docs/cambridge.md +++ b/docs/cambridge.md @@ -1,4 +1,5 @@ # 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 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, From e1b1402f501a1443eceacc0d2e3476b92008e9b8 Mon Sep 17 00:00:00 2001 From: Anthony Underwood Date: Sat, 24 Apr 2021 13:22:54 +0100 Subject: [PATCH 4/4] Add Cambridge to README --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 7637725..61e7acc 100644 --- a/README.md +++ b/README.md @@ -100,6 +100,7 @@ Currently documentation is available for the following systems: * [BI](docs/bi.md) * [BINAC](docs/binac.md) * [BIOHPC_GEN](docs/biohpc_gen.md) +* [CAMBRIDGE](docs/cambridge.md) * [CBE](docs/cbe.md) * [CCGA_DX](docs/ccga_dx.md) * [CCGA_MED](docs/ccga_med.md)