From 429c7b4fa82190fbf8aa26981989627f037ea97d Mon Sep 17 00:00:00 2001 From: Spix Date: Mon, 7 Mar 2022 15:01:46 -0500 Subject: [PATCH 1/4] initial commit --- .github/workflows/main.yml | 1 + README.md | 1 + conf/vai.config | 23 +++++++++++++++++++++++ docs/vai.md | 14 ++++++++++++++ nfcore_custom.config | 1 + 5 files changed, 40 insertions(+) create mode 100644 conf/vai.config create mode 100644 docs/vai.md diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index b9df947..6117514 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -70,6 +70,7 @@ jobs: - 'utd_ganymede' - 'utd_sysbio' - 'uzh' + - 'vai' steps: - uses: actions/checkout@v1 - name: Install Nextflow diff --git a/README.md b/README.md index c5a411c..51bbb5d 100644 --- a/README.md +++ b/README.md @@ -137,6 +137,7 @@ Currently documentation is available for the following systems: * [UTD_GANYMEDE](docs/utd_ganymede.md) * [UTD_SYSBIO](docs/utd_sysbio.md) * [UZH](docs/uzh.md) +* [VAI](docs/vai.md) ### Uploading to `nf-core/configs` diff --git a/conf/vai.config b/conf/vai.config new file mode 100644 index 0000000..3563eb4 --- /dev/null +++ b/conf/vai.config @@ -0,0 +1,23 @@ +params { + config_profile_description = 'Van Andel Institute HPC profile provided by nf-core/configs.' + config_profile_contact = 'Nathan Spix (@njspix)' + config_profile_url = 'https://vanandelinstitute.sharepoint.com/sites/SC/SitePages/HPC3-High-Performance-Cluster-and-Cloud-Computing.aspx' + max_memory = 250.GB + max_cpus = 40 + max_time = 640.h +} + +process { + beforeScript = 'module load singularity' + executor = 'pbs' + queue = { task.time <= 48.h ? 'shortq' : 'longq' } + maxRetries = 2 +} + +singularity { + enabled = true + autoMounts = true +} + + + diff --git a/docs/vai.md b/docs/vai.md new file mode 100644 index 0000000..b174bbf --- /dev/null +++ b/docs/vai.md @@ -0,0 +1,14 @@ +# nf-core/configs: VAI configuration + +All nf-core pipelines have been successfully configured for use on the HPC cluster at Van Andel Institute. + +To use, run the pipeline with `-profile vai`. This will download and launch the [`vai.config`](../conf/vai.config) which has been pre-configured with a setup suitable for the VAI HPC. 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. + +```bash +module load singularity +NXF_OPTS="-Xmx500m" MALLOC_ARENA_MAX=4 nextflow run +``` + +>NB: You will need an account to use the HPC 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 the login node. If in doubt contact IT. +>NB: The submit node limits the amount of memory available to each user. The `NXF_OPTS` and `MALLOC_ARENA_MAX` parameters above prevent Nextflow from allocating more memory than the scheduler will allow. diff --git a/nfcore_custom.config b/nfcore_custom.config index 8781766..4f8f506 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -64,4 +64,5 @@ profiles { utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" } utd_sysbio { includeConfig "${params.custom_config_base}/conf/utd_sysbio.config" } uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" } + vai { includeConfig "${params.custom_config_base}/conf/vai.config" } } From c97c48ae5b597fd27a9733a7bf5226ae069488fb Mon Sep 17 00:00:00 2001 From: Spix Date: Mon, 7 Mar 2022 15:11:45 -0500 Subject: [PATCH 2/4] update singularity command --- conf/vai.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/vai.config b/conf/vai.config index 3563eb4..2cef179 100644 --- a/conf/vai.config +++ b/conf/vai.config @@ -8,7 +8,7 @@ params { } process { - beforeScript = 'module load singularity' + beforeScript = 'alias singularity /varidata/research/software/singularity/singularity-ce-3.8.2/bin/singularity' executor = 'pbs' queue = { task.time <= 48.h ? 'shortq' : 'longq' } maxRetries = 2 From 17c77ad516db4f38776cb02b87e4354e307cbd88 Mon Sep 17 00:00:00 2001 From: Spix Date: Mon, 7 Mar 2022 15:13:26 -0500 Subject: [PATCH 3/4] update singularity command --- conf/vai.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/vai.config b/conf/vai.config index 2cef179..4ba037e 100644 --- a/conf/vai.config +++ b/conf/vai.config @@ -8,7 +8,7 @@ params { } process { - beforeScript = 'alias singularity /varidata/research/software/singularity/singularity-ce-3.8.2/bin/singularity' + beforeScript = 'alias singularity=/varidata/research/software/singularity/singularity-ce-3.8.2/bin/singularity' executor = 'pbs' queue = { task.time <= 48.h ? 'shortq' : 'longq' } maxRetries = 2 From d067f61329ae8811c8ab85424ba8339e30f16f70 Mon Sep 17 00:00:00 2001 From: Nathan Spix <56930974+njspix@users.noreply.github.com> Date: Mon, 7 Mar 2022 15:22:18 -0500 Subject: [PATCH 4/4] remove extra spaces --- conf/vai.config | 3 --- 1 file changed, 3 deletions(-) diff --git a/conf/vai.config b/conf/vai.config index 4ba037e..fcc63b3 100644 --- a/conf/vai.config +++ b/conf/vai.config @@ -18,6 +18,3 @@ singularity { enabled = true autoMounts = true } - - -