From f8b932ae2d5cf97aa2a2a290ec6b1ee1ca45a650 Mon Sep 17 00:00:00 2001 From: Matiss Ozols Date: Thu, 21 Oct 2021 18:32:57 +0100 Subject: [PATCH 1/7] added leicester profile --- conf/leicester.conf | 16 ++++++++++++++++ docs/leicester.md | 8 ++++++++ nfcore_custom.config | 1 + 3 files changed, 25 insertions(+) create mode 100644 conf/leicester.conf create mode 100644 docs/leicester.md diff --git a/conf/leicester.conf b/conf/leicester.conf new file mode 100644 index 0000000..d91a006 --- /dev/null +++ b/conf/leicester.conf @@ -0,0 +1,16 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'ALICE and SPECTRE cluster profile provided by nf-core/configs.' + config_profile_contact = 'Matiss Ozols - mo246@leichester.ac.uk | mo11@sanger.ac.uk | matiss.ozols@manchester.ac.uk | mo513@cam.ac.uk' +} + +singularity { + enabled = true + envWhitelist = 'TZ' +} + +process { + executor = 'pbs' + queue = { task.time <= 24.h ? 'short' : task.time > 672.h ? 'long' : 'medium'} +} + diff --git a/docs/leicester.md b/docs/leicester.md new file mode 100644 index 0000000..3118022 --- /dev/null +++ b/docs/leicester.md @@ -0,0 +1,8 @@ +# nf-core/configs: Leicester Configuration + +All nf-core pipelines have been successfully configured for use on the ALICE and SPECTRE cluster at the University of Leicester. Read more about lLicester HPC - https://uniofleicester.sharepoint.com/sites/research-computing/SitePages/alice.aspx + +To use, run the pipeline with `-profile leicester`. This will download and launch the [`leicester.config`](../conf/leicester.config) which has been pre-configured with a setup suitable for the Leicester 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. + +>NB: You will need an account to use the ALICE and SPECTRE cluster in order to run the pipeline. If in doubt contact IT. +>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. \ No newline at end of file diff --git a/nfcore_custom.config b/nfcore_custom.config index eb5b509..caf1679 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -19,6 +19,7 @@ profiles { binac { includeConfig "${params.custom_config_base}/conf/binac.config" } biohpc_gen { includeConfig "${params.custom_config_base}/conf/biohpc_gen.config" } cambridge { includeConfig "${params.custom_config_base}/conf/cambridge.config" } + leicester { includeConfig "${params.custom_config_base}/conf/leicester.config" } cbe { includeConfig "${params.custom_config_base}/conf/cbe.config" } ccga_dx { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" } ccga_med { includeConfig "${params.custom_config_base}/conf/ccga_med.config" } From e9ba223103951d9bdc7f7ed27a6996fed974f91e Mon Sep 17 00:00:00 2001 From: Matiss Ozols Date: Thu, 21 Oct 2021 18:55:03 +0100 Subject: [PATCH 2/7] added leicester profile --- .github/workflows/main.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 382a0f7..03229cc 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -26,6 +26,7 @@ jobs: - 'binac' - 'biohpc_gen' - 'cambridge' + - 'leicester' - 'cbe' - 'ccga_dx' - 'ccga_med' From e8ce4fe8df0228eec7a70bc40562a482e3baadce Mon Sep 17 00:00:00 2001 From: Matiss Ozols Date: Thu, 21 Oct 2021 18:59:17 +0100 Subject: [PATCH 3/7] added leicester profile --- conf/leicester.config | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 conf/leicester.config diff --git a/conf/leicester.config b/conf/leicester.config new file mode 100644 index 0000000..d91a006 --- /dev/null +++ b/conf/leicester.config @@ -0,0 +1,16 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'ALICE and SPECTRE cluster profile provided by nf-core/configs.' + config_profile_contact = 'Matiss Ozols - mo246@leichester.ac.uk | mo11@sanger.ac.uk | matiss.ozols@manchester.ac.uk | mo513@cam.ac.uk' +} + +singularity { + enabled = true + envWhitelist = 'TZ' +} + +process { + executor = 'pbs' + queue = { task.time <= 24.h ? 'short' : task.time > 672.h ? 'long' : 'medium'} +} + From d45a06a6817ccbe3bf5e75fa22b1ae266cca68a0 Mon Sep 17 00:00:00 2001 From: Matiss Ozols Date: Thu, 21 Oct 2021 19:02:13 +0100 Subject: [PATCH 4/7] added leicester profile --- conf/leicester.conf | 16 ---------------- 1 file changed, 16 deletions(-) delete mode 100644 conf/leicester.conf diff --git a/conf/leicester.conf b/conf/leicester.conf deleted file mode 100644 index d91a006..0000000 --- a/conf/leicester.conf +++ /dev/null @@ -1,16 +0,0 @@ -//Profile config names for nf-core/configs -params { - config_profile_description = 'ALICE and SPECTRE cluster profile provided by nf-core/configs.' - config_profile_contact = 'Matiss Ozols - mo246@leichester.ac.uk | mo11@sanger.ac.uk | matiss.ozols@manchester.ac.uk | mo513@cam.ac.uk' -} - -singularity { - enabled = true - envWhitelist = 'TZ' -} - -process { - executor = 'pbs' - queue = { task.time <= 24.h ? 'short' : task.time > 672.h ? 'long' : 'medium'} -} - From 98a69683c2f59aa2018f9031b3cafd1959a97017 Mon Sep 17 00:00:00 2001 From: Matiss Ozols Date: Thu, 21 Oct 2021 19:04:48 +0100 Subject: [PATCH 5/7] added leicester profile --- docs/leicester.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/leicester.md b/docs/leicester.md index 3118022..72947f9 100644 --- a/docs/leicester.md +++ b/docs/leicester.md @@ -2,7 +2,7 @@ All nf-core pipelines have been successfully configured for use on the ALICE and SPECTRE cluster at the University of Leicester. Read more about lLicester HPC - https://uniofleicester.sharepoint.com/sites/research-computing/SitePages/alice.aspx -To use, run the pipeline with `-profile leicester`. This will download and launch the [`leicester.config`](../conf/leicester.config) which has been pre-configured with a setup suitable for the Leicester 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. +To use, run the pipeline with `-profile leicester`. This will download and launch the [`leicester.config`](../conf/leicester.config ) which has been pre-configured with a setup suitable for the Leicester 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. >NB: You will need an account to use the ALICE and SPECTRE cluster in order to run the pipeline. If in doubt contact IT. >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. \ No newline at end of file From 1f58ea42c731488c00a7768fdbdfb8f1186c19d4 Mon Sep 17 00:00:00 2001 From: Matiss Ozols Date: Thu, 21 Oct 2021 19:06:03 +0100 Subject: [PATCH 6/7] added leicester profile --- docs/leicester.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/leicester.md b/docs/leicester.md index 72947f9..829bc00 100644 --- a/docs/leicester.md +++ b/docs/leicester.md @@ -5,4 +5,4 @@ All nf-core pipelines have been successfully configured for use on the ALICE and To use, run the pipeline with `-profile leicester`. This will download and launch the [`leicester.config`](../conf/leicester.config ) which has been pre-configured with a setup suitable for the Leicester 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. >NB: You will need an account to use the ALICE and SPECTRE cluster in order to run the pipeline. If in doubt contact IT. ->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. \ No newline at end of file +>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 5222d7ed9bf1773d23ca60df2fd2472c81c224c8 Mon Sep 17 00:00:00 2001 From: Matiss Ozols Date: Thu, 21 Oct 2021 19:08:06 +0100 Subject: [PATCH 7/7] added leicester profile --- docs/leicester.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/leicester.md b/docs/leicester.md index 829bc00..79445af 100644 --- a/docs/leicester.md +++ b/docs/leicester.md @@ -1,6 +1,6 @@ # nf-core/configs: Leicester Configuration -All nf-core pipelines have been successfully configured for use on the ALICE and SPECTRE cluster at the University of Leicester. Read more about lLicester HPC - https://uniofleicester.sharepoint.com/sites/research-computing/SitePages/alice.aspx +All nf-core pipelines have been successfully configured for use on the ALICE and SPECTRE cluster at the University of Leicester. To use, run the pipeline with `-profile leicester`. This will download and launch the [`leicester.config`](../conf/leicester.config ) which has been pre-configured with a setup suitable for the Leicester 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.