From ca1428f7d9459f01adf307fa024746aed15847a0 Mon Sep 17 00:00:00 2001 From: dmarron Date: Tue, 22 Aug 2023 13:16:17 -0400 Subject: [PATCH 1/4] add unc_lccc.config --- conf/unc_lccc.config | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 conf/unc_lccc.config diff --git a/conf/unc_lccc.config b/conf/unc_lccc.config new file mode 100644 index 000000000..f32923e13 --- /dev/null +++ b/conf/unc_lccc.config @@ -0,0 +1,20 @@ +params { + config_profile_description = 'The Lineberger Comprehensive Cancer Center at the University of North Carolina at Chapel Hill' + config_profile_contact = 'Alan Hoyle (@alanhoyle)' + config_profile_url = 'https://lbc.unc.edu' + singularity_library_dir = '/datastore/lbcfs/labs/bioinformatics/software/singularity-library' + } + +process { + executor = "slurm" + queue = "allnodes" +} +singularity{ + enabled = true + autoMounts = true + runOptions = '-B /datastore' +} +params { + max_memory = 950.GB + max_cpus = 90 + } From 64237ba4d73530fa6bed8b38583214700efd5eaf Mon Sep 17 00:00:00 2001 From: dmarron Date: Tue, 22 Aug 2023 13:29:37 -0400 Subject: [PATCH 2/4] add docs/unc_lccc.md --- .github/workflows/main.yml | 1 + README.md | 1 + docs/unc_lccc.md | 24 ++++++++++++++++++++++++ nfcore_custom.config | 1 + 4 files changed, 27 insertions(+) create mode 100644 docs/unc_lccc.md diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 7e37e31b2..75d672450 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -114,6 +114,7 @@ jobs: - "ucd_sonic" - "uge" - "unibe_ibu" + - "unc_lccc" - "uppmax" - "utd_ganymede" - "utd_sysbio" diff --git a/README.md b/README.md index b7a3d0109..ed2fb4284 100644 --- a/README.md +++ b/README.md @@ -167,6 +167,7 @@ Currently documentation is available for the following systems: - [UCD_SONIC](docs/ucd_sonic.md) - [UCL_MYRIAD](docs/ucl_myriad.md) - [UCT_HPC](docs/uct_hpc.md) +- [UNC_LCCC](docs/unc_lccc.md) - [UGE](docs/uge.md) - [UNIBE_IBU](docs/unibe_ibu.md) - [UPPMAX](docs/uppmax.md) diff --git a/docs/unc_lccc.md b/docs/unc_lccc.md new file mode 100644 index 000000000..1afad1514 --- /dev/null +++ b/docs/unc_lccc.md @@ -0,0 +1,24 @@ +# nf-core/configs: PROFILE Configuration + +All nf-core pipelines have been successfully configured for use on the Lineberger Bioinformatics Group cluster at the University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center. + +To use, run the pipeline with `-profile unc_lccc`. This will download and launch the [`unc_lccc.config`](../conf/unc_lccc.config) which has been pre-configured with a setup suitable for the LBG cluster. Using this profile, docker images containing all of the required software will be downloaded, and converted to a Singularity/Apptainer image before execution of the pipeline. + +## Below are non-mandatory information e.g. on modules to load etc + +Before running pipelines you will need to login to a compute node and install nextflow https://www.nextflow.io/. You can do this by issuing the commands below: + +```bash +## install Nextflow +module purge +module load Nextflow/0.32.0 +module load Singularity/2.6.0 +``` + +## Below are non-mandatory information on iGenomes specific configuration + +A local copy of the iGenomes resource has been made available on PROFILE CLUSTER so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. +You can do this by simply using the `--genome ` parameter. + +> NB: You will need an account to use the in order to run the pipelines. If in doubt contact . +> 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. diff --git a/nfcore_custom.config b/nfcore_custom.config index 8c205dc66..9514739dc 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -95,6 +95,7 @@ profiles { ucl_myriad { includeConfig "${params.custom_config_base}/conf/ucl_myriad.config"} uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" } uge { includeConfig "${params.custom_config_base}/conf/uge.config" } + unc_lccc { includeConfig "${params.custom_config_base}/conf/unc_lccc.config" } unibe_ibu { includeConfig "${params.custom_config_base}/conf/unibe_ibu.config" } uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" } utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" } From 4ca50afadbdfff039e1e62581eb82c9eeba2683b Mon Sep 17 00:00:00 2001 From: dmarron Date: Tue, 22 Aug 2023 17:07:00 -0400 Subject: [PATCH 3/4] Remove iGenomes message from unc_lccc.md --- docs/unc_lccc.md | 5 ----- 1 file changed, 5 deletions(-) diff --git a/docs/unc_lccc.md b/docs/unc_lccc.md index 1afad1514..5d601a2cf 100644 --- a/docs/unc_lccc.md +++ b/docs/unc_lccc.md @@ -15,10 +15,5 @@ module load Nextflow/0.32.0 module load Singularity/2.6.0 ``` -## Below are non-mandatory information on iGenomes specific configuration - -A local copy of the iGenomes resource has been made available on PROFILE CLUSTER so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. -You can do this by simply using the `--genome ` parameter. - > NB: You will need an account to use the in order to run the pipelines. If in doubt contact . > 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 f561710b9f8a52a67b7fef27f79f5f13c0b1f4bb Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 23 Aug 2023 07:25:01 +0200 Subject: [PATCH 4/4] Fix linting --- docs/unc_lccc.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/unc_lccc.md b/docs/unc_lccc.md index 5d601a2cf..0287bf6d4 100644 --- a/docs/unc_lccc.md +++ b/docs/unc_lccc.md @@ -15,5 +15,5 @@ module load Nextflow/0.32.0 module load Singularity/2.6.0 ``` -> NB: You will need an account to use the in order to run the pipelines. If in doubt contact . +> NB: You will need an account to use the in order to run the pipelines. If in doubt contact . > 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.