From b638694bd07aad57a70ca0c06158bff358df114f Mon Sep 17 00:00:00 2001 From: Nathan Watson-Haigh Date: Sat, 12 Mar 2022 21:17:33 +1030 Subject: [PATCH 1/7] Added SAHMRI HPC profile --- .github/workflows/main.yml | 1 + conf/sahmri.config | 28 ++++++++++++++++++++++++++++ docs/sahmri.md | 0 3 files changed, 29 insertions(+) create mode 100644 conf/sahmri.config create mode 100644 docs/sahmri.md diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 28776fd..01b24d9 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -63,6 +63,7 @@ jobs: - 'phoenix' - 'prince' - 'rosalind' + - 'sahmri' - 'sanger' - 'seg_globe' - 'uct_hpc' diff --git a/conf/sahmri.config b/conf/sahmri.config new file mode 100644 index 0000000..85ff1fa --- /dev/null +++ b/conf/sahmri.config @@ -0,0 +1,28 @@ +params { + config_profile_description = 'South Australian Medial Health and Research Institute (SAHMRI) HPC cluster profile.' + config_profile_contact = 'Nathan Watson-Haigh (nathan.watson-haigh@sahmri.com)' + config_profile_url = "https://sahmri.com" + max_memory = 375.GB + max_cpus = 32 + max_time = 14.d + igenomes_base = '/cancer/storage/shared/igenomes/' +} +process { + executor = 'slurm' + queue = 'sahmri_prod_hpc,sahmri_cancer_hpc' + maxRetries = 2 + + cpus = { check_max( 2 * task.attempt, 'cpus') } + memory = { check_max( 1.GB * task.attempt, 'memory') } + time = { check_max( 10.m * task.attempt, 'time') } +} +executor { + queueSize = 50 + submitRateLimit = '10 sec' +} +singularity { + enabled = true + autoMounts = true + cacheDir = '/cancer/storage/shared/simg' +} +cleanup = true diff --git a/docs/sahmri.md b/docs/sahmri.md new file mode 100644 index 0000000..e69de29 From b58a9952be938da8b3951f75af471e42747cbc78 Mon Sep 17 00:00:00 2001 From: Nathan Watson-Haigh Date: Sat, 12 Mar 2022 21:24:05 +1030 Subject: [PATCH 2/7] Added SAHMRI HPC profile --- nfcore_custom.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nfcore_custom.config b/nfcore_custom.config index 2c25adb..d3adc4f 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -57,6 +57,7 @@ profiles { phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } prince { includeConfig "${params.custom_config_base}/conf/prince.config" } rosalind { includeConfig "${params.custom_config_base}/conf/rosalind.config" } + sahmri { includeConfig "${params.custom_config_base}/conf/sahmri.config" } sanger { includeConfig "${params.custom_config_base}/conf/sanger.config"} seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"} uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" } From dba3fb4c1d51996b02c0451222937a2d06fd0e41 Mon Sep 17 00:00:00 2001 From: Nathan Watson-Haigh Date: Sun, 13 Mar 2022 00:05:34 +1030 Subject: [PATCH 3/7] Added SAHMRI HPC profile docs --- docs/sahmri.md | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/docs/sahmri.md b/docs/sahmri.md index e69de29..4ef285e 100644 --- a/docs/sahmri.md +++ b/docs/sahmri.md @@ -0,0 +1,18 @@ +# nf-core/configs: SAHMRI HPC Configuration + +All nf-core pipelines have been successfully configured for use on the HPC cluster at [SAHMRI](https://sahmri.org.au/). +To use, run the pipeline with `-profile sahmri`. This will download and launch the [`sahmri.config`](../conf/sahmri.config) which has been pre-configured +with a setup suitable for the SAHMRI 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 SAHMRI 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 SAHMRI HPC cluster in order to run the pipeline. If in doubt contact the ICT Service Desk. +> NB: Nextflow will need to submit the jobs via SLURM to the SAHMRI HPC cluster and as such the commands above will have to be executed on the login +node. If in doubt contact ICT. From 2f0b0225716017703209be1dd5ca7d3794004f5d Mon Sep 17 00:00:00 2001 From: Nathan Watson-Haigh Date: Sun, 13 Mar 2022 00:08:42 +1030 Subject: [PATCH 4/7] Fixed typos --- conf/sahmri.config | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/sahmri.config b/conf/sahmri.config index 85ff1fa..6757dbf 100644 --- a/conf/sahmri.config +++ b/conf/sahmri.config @@ -1,7 +1,7 @@ params { - config_profile_description = 'South Australian Medial Health and Research Institute (SAHMRI) HPC cluster profile.' - config_profile_contact = 'Nathan Watson-Haigh (nathan.watson-haigh@sahmri.com)' - config_profile_url = "https://sahmri.com" + config_profile_description = 'South Australian Health and Medical Research Institute (SAHMRI) HPC cluster profile.' + config_profile_contact = 'Nathan Watson-Haigh (nathan.watson-haigh@sahmri.com)' + config_profile_url = "https://sahmri.org.au" max_memory = 375.GB max_cpus = 32 max_time = 14.d From cc550267516618430ac80afb6fd300173a0c54d2 Mon Sep 17 00:00:00 2001 From: Nathan Watson-Haigh Date: Sun, 13 Mar 2022 07:39:31 +1030 Subject: [PATCH 5/7] Add singularity to PATH --- conf/sahmri.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/sahmri.config b/conf/sahmri.config index 6757dbf..ad6b84d 100644 --- a/conf/sahmri.config +++ b/conf/sahmri.config @@ -23,6 +23,7 @@ executor { singularity { enabled = true autoMounts = true + beforeScript = 'export PATH=/apps/opt/singularity/latest/bin:${PATH}' cacheDir = '/cancer/storage/shared/simg' } cleanup = true From a0f5ac744581085a73190180ce5fcca4c0b877fe Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Tue, 15 Mar 2022 11:41:51 +1030 Subject: [PATCH 6/7] Added references subdir to igenomes_base --- conf/sahmri.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/sahmri.config b/conf/sahmri.config index ad6b84d..b3eb8c6 100644 --- a/conf/sahmri.config +++ b/conf/sahmri.config @@ -5,7 +5,7 @@ params { max_memory = 375.GB max_cpus = 32 max_time = 14.d - igenomes_base = '/cancer/storage/shared/igenomes/' + igenomes_base = '/cancer/storage/shared/igenomes/references/' } process { executor = 'slurm' From 30f710ada44884596061cbb0069e68a08e26a242 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Thu, 17 Mar 2022 13:38:43 +1030 Subject: [PATCH 7/7] Add debug profile --- conf/sahmri.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/conf/sahmri.config b/conf/sahmri.config index b3eb8c6..b47db52 100644 --- a/conf/sahmri.config +++ b/conf/sahmri.config @@ -27,3 +27,8 @@ singularity { cacheDir = '/cancer/storage/shared/simg' } cleanup = true +profiles { + debug { + cleanup = false + } +}