From b69c587a566140cbbb1b4f95cc15da48dd3f79cd Mon Sep 17 00:00:00 2001 From: Charlie Whittaker <49070063+bumproo@users.noreply.github.com> Date: Sat, 11 Jan 2025 14:30:26 -0500 Subject: [PATCH 01/11] Create ki_luria.conf --- conf/ki_luria.conf | 1 + 1 file changed, 1 insertion(+) create mode 100644 conf/ki_luria.conf diff --git a/conf/ki_luria.conf b/conf/ki_luria.conf new file mode 100644 index 000000000..8b1378917 --- /dev/null +++ b/conf/ki_luria.conf @@ -0,0 +1 @@ + From 31f9ae41de3a1834686d30b0e0a98677da0ca0f0 Mon Sep 17 00:00:00 2001 From: Charlie Whittaker <49070063+bumproo@users.noreply.github.com> Date: Sat, 11 Jan 2025 14:30:57 -0500 Subject: [PATCH 02/11] Create ki_luria.md --- docs/ki_luria.md | 1 + 1 file changed, 1 insertion(+) create mode 100644 docs/ki_luria.md diff --git a/docs/ki_luria.md b/docs/ki_luria.md new file mode 100644 index 000000000..8b1378917 --- /dev/null +++ b/docs/ki_luria.md @@ -0,0 +1 @@ + From 99af2e444cb4ba162f53f3dbb295c645bcd126eb Mon Sep 17 00:00:00 2001 From: Charlie Whittaker <49070063+bumproo@users.noreply.github.com> Date: Sat, 11 Jan 2025 14:36:30 -0500 Subject: [PATCH 03/11] Update nfcore_custom.config --- nfcore_custom.config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/nfcore_custom.config b/nfcore_custom.config index 4c9d6d987..e53138ff5 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -217,6 +217,9 @@ profiles { kaust { includeConfig "${params.custom_config_base}/conf/kaust.config" } + ki_luria { + includeConfig "${params.custom_config_base}/conf/ki_luria.config" + } leicester { includeConfig "${params.custom_config_base}/conf/leicester.config" } From be564f9f3bc9be1a995ae1564e8797d960925977 Mon Sep 17 00:00:00 2001 From: Charlie Whittaker <49070063+bumproo@users.noreply.github.com> Date: Sat, 11 Jan 2025 14:37:50 -0500 Subject: [PATCH 04/11] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index a8d07d67e..f6573747b 100644 --- a/README.md +++ b/README.md @@ -155,6 +155,7 @@ Currently documentation is available for the following systems: - [UNSW_Katana](docs/unsw_katana.md) - [KU SUND DANHEAD](docs/ku_sund_danhead.md) - [KAUST](docs/kaust.md) +- [KI_LURIA](docs/ki_luria.md) - [LUGH](docs/lugh.md) - [M3C](docs/m3c.md) - [MAESTRO](docs/maestro.md) From cad97f976864d86c3556ab30be9dbb7efb46f459 Mon Sep 17 00:00:00 2001 From: Charlie Whittaker <49070063+bumproo@users.noreply.github.com> Date: Sat, 11 Jan 2025 14:38:37 -0500 Subject: [PATCH 05/11] Update main.yml --- .github/workflows/main.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 25e303bdb..299f3e5ed 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -103,6 +103,7 @@ jobs: - "unsw_katana" - "ku_sund_danhead" - "kaust" + - "ki_luria" - "leicester" - "lugh" - "m3c" From 0a4ab72420c8ca9cef561750f800369cfc04a353 Mon Sep 17 00:00:00 2001 From: Charlie Whittaker <49070063+bumproo@users.noreply.github.com> Date: Sat, 11 Jan 2025 14:48:18 -0500 Subject: [PATCH 06/11] Update ki_luria.conf --- conf/ki_luria.conf | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/conf/ki_luria.conf b/conf/ki_luria.conf index 8b1378917..3c345d3cd 100644 --- a/conf/ki_luria.conf +++ b/conf/ki_luria.conf @@ -1 +1,27 @@ +// Nextflow config for running on the Koch Institute of MIT Luria HPC cluster +params { + config_profile_description = 'KI at MIT Luria HPC cluster profile.' + config_profile_contact = 'Charlie Whittaker (@Charlie14557807)' + config_profile_url = "https://igb.mit.edu/computing-resources/luria-cluster" +} +singularity { + enabled = true + autoMounts = true +} + +process { + resourceLimits = [ + memory: 64.GB, + cpus: 16, + time: 12.h + ] + executor = 'slurm' + clusterOptions = '-p normal' +} + +params { + max_memory = 64.GB + max_cpus = 16 + max_time = 12.h +} From e92bccab0879340289452906c6674c7dcce0a6a3 Mon Sep 17 00:00:00 2001 From: Charlie Whittaker <49070063+bumproo@users.noreply.github.com> Date: Sat, 11 Jan 2025 14:59:17 -0500 Subject: [PATCH 07/11] Update ki_luria.md --- docs/ki_luria.md | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/docs/ki_luria.md b/docs/ki_luria.md index 8b1378917..b5f6ffcee 100644 --- a/docs/ki_luria.md +++ b/docs/ki_luria.md @@ -1 +1,19 @@ +# nf-core/configs: KI at MIT Luria Configuration +All nf-core pipelines have been successfully configured for use on the [KI at MIT Luria Cluster](https://igb.mit.edu/computing-resources/luria-cluster). + +To use, run the pipeline with `-profile ki_luria`. This will download and launch the [`ki_luria.config`](../conf/ki_luria.config) which has been pre-configured with a setup suitable for the Luria 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. + +## Below are non-mandatory information e.g. on modules to load etc + +Before running the pipeline you will need to activate the Nextflow conda environment and load Singularity using the environment module system on Luria Cluster. You can do this by issuing the commands below: + +```bash +module add miniconda3/v4 +source /home/software/conda/miniconda3/bin/condainit +conda activate /home/charliew/.conda/envs/nf-core_Oct24 +module add singularity/3.10.4 +``` + +> NB: You will need an account to use the HPC cluster on Lura in order to run the pipeline. +> 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. From 4ff10798d466798f3ca2ff0e93912413509177e5 Mon Sep 17 00:00:00 2001 From: Charlie Whittaker <49070063+bumproo@users.noreply.github.com> Date: Tue, 14 Jan 2025 06:57:51 -0500 Subject: [PATCH 08/11] Rename ki_luria.conf to ki_luria.config --- conf/{ki_luria.conf => ki_luria.config} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename conf/{ki_luria.conf => ki_luria.config} (100%) diff --git a/conf/ki_luria.conf b/conf/ki_luria.config similarity index 100% rename from conf/ki_luria.conf rename to conf/ki_luria.config From bcb822d5e1911bd0c282f1236b0ebbf45737381b Mon Sep 17 00:00:00 2001 From: Charlie Whittaker <49070063+bumproo@users.noreply.github.com> Date: Tue, 14 Jan 2025 07:55:31 -0500 Subject: [PATCH 09/11] Update ki_luria.config --- conf/ki_luria.config | 5 ----- 1 file changed, 5 deletions(-) diff --git a/conf/ki_luria.config b/conf/ki_luria.config index 3c345d3cd..d348ccd3e 100644 --- a/conf/ki_luria.config +++ b/conf/ki_luria.config @@ -20,8 +20,3 @@ process { clusterOptions = '-p normal' } -params { - max_memory = 64.GB - max_cpus = 16 - max_time = 12.h -} From ca4ce9e3edc5ceac4e46b41166929512965f7894 Mon Sep 17 00:00:00 2001 From: Charlie Whittaker <49070063+bumproo@users.noreply.github.com> Date: Tue, 14 Jan 2025 08:32:34 -0500 Subject: [PATCH 10/11] Adding before script to ki_luria.config --- conf/ki_luria.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/ki_luria.config b/conf/ki_luria.config index d348ccd3e..4d3401512 100644 --- a/conf/ki_luria.config +++ b/conf/ki_luria.config @@ -18,5 +18,6 @@ process { ] executor = 'slurm' clusterOptions = '-p normal' + beforeScript = 'module add miniconda3/v4;source /home/software/conda/miniconda3/bin/condainit;conda activate /home/charliew/.conda/envs/nf-core_Oct24;module add singularity/3.10.4' } From 85a9b67727a51bdcec80dd0c1924131051122e88 Mon Sep 17 00:00:00 2001 From: Charlie Whittaker <49070063+bumproo@users.noreply.github.com> Date: Tue, 14 Jan 2025 09:00:43 -0500 Subject: [PATCH 11/11] removing beforeScript in ki_luria.config --- conf/ki_luria.config | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/ki_luria.config b/conf/ki_luria.config index 4d3401512..d348ccd3e 100644 --- a/conf/ki_luria.config +++ b/conf/ki_luria.config @@ -18,6 +18,5 @@ process { ] executor = 'slurm' clusterOptions = '-p normal' - beforeScript = 'module add miniconda3/v4;source /home/software/conda/miniconda3/bin/condainit;conda activate /home/charliew/.conda/envs/nf-core_Oct24;module add singularity/3.10.4' }