From 123c44c56daf8fa6f06ed46a2f6ca454ddc653ca Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 9 Mar 2020 16:18:41 -0500 Subject: [PATCH 1/4] feat: add initial ganymede config --- conf/utd_ganymede.config | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 conf/utd_ganymede.config diff --git a/conf/utd_ganymede.config b/conf/utd_ganymede.config new file mode 100644 index 0000000..a183861 --- /dev/null +++ b/conf/utd_ganymede.config @@ -0,0 +1,24 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'University of Texas at Dallas HPC cluster profile provided by nf-core/configs' + config_profile_contact = 'Edmund Miller(@emiller88)' + config_profile_url = 'http://docs.oithpc.utdallas.edu/' +} + +singularity { + enabled = true + envWhitelist='SINGULARITY_BINDPATH' + autoMounts = true +} + +process { + beforeScript = 'module load Singularity/2.4.5' + executor = 'slurm' + queue = 'genomics' +} + +params { + max_memory = 32.GB + max_cpus = 16 + max_time = 48.h +} From 1c623953322329c05345517940a5d19fbf678fb9 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 9 Mar 2020 20:07:46 -0500 Subject: [PATCH 2/4] docs(utd_ganymede): add initial documentation --- README.md | 1 + docs/utd_ganymede.md | 18 ++++++++++++++++++ nfcore_custom.config | 4 +++- 3 files changed, 22 insertions(+), 1 deletion(-) create mode 100644 docs/utd_ganymede.md diff --git a/README.md b/README.md index 755b1d2..686b157 100644 --- a/README.md +++ b/README.md @@ -117,6 +117,7 @@ Currently documentation is available for the following systems: * [SHH](docs/shh.md) * [UCT_HEX](docs/uct_hex.md) * [UPPMAX](docs/uppmax.md) +* [UTD_GANYMEDE](docs/utd_ganymede.md) * [UZH](docs/uzh.md) ### Uploading to `nf-core/configs` diff --git a/docs/utd_ganymede.md b/docs/utd_ganymede.md new file mode 100644 index 0000000..81dd46a --- /dev/null +++ b/docs/utd_ganymede.md @@ -0,0 +1,18 @@ +# nf-core/configs: UTD Ganymede Configuration + +All nf-core pipelines have been successfully configured for use on the Ganymede HPC cluster at the [The Univeristy of Texas at Dallas](https://www.utdallas.edu/). + +To use, run the pipeline with `-profile utd_ganymede`. This will download and launch the [`utd_ganymede.config`](../conf/utd_ganymede.config) which has been pre-configured with a setup suitable for the Ganymede HPC 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. + +Before running the pipeline you will need to load Singularity using the environment module system on Ganymede. You can do this by issuing the commands below: + +```bash +## Singularity environment modules +module purge +module load singularity +``` + +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 HPC cluster on Ganymede in order to run the pipeline. If in doubt contact Ganymedeadmins. +>NB: Nextflow will need to submit the jobs via SLURM 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 GanymedeAdmins. diff --git a/nfcore_custom.config b/nfcore_custom.config index 848db80..383eaf0 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -37,6 +37,7 @@ profiles { shh { includeConfig "${params.custom_config_base}/conf/shh.config" } uct_hex { includeConfig "${params.custom_config_base}/conf/uct_hex.config" } uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" } + utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" } uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" } } @@ -50,6 +51,7 @@ params { crick: ['.thecrick.org'], genotoul: ['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest: ['.genouest.org'], - uppmax: ['.uppmax.uu.se'] + uppmax: ['.uppmax.uu.se'], + utd_ganymede: ['ganymede.utdallas.edu'] ] } From b79f0f0a21f017e21d07bba4816620a41063c31d Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 9 Mar 2020 20:11:52 -0500 Subject: [PATCH 3/4] ci: add utd_gaymede to main --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 042dd26..0917dd2 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: matrix: - profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh'] + profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'utd_ganymede', 'uzh'] steps: - uses: actions/checkout@v1 - name: Install Nextflow From c42bb079817a84f87144fcbe6c386419a327ff4c Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 10 Mar 2020 09:55:17 -0500 Subject: [PATCH 4/4] fix: Singularity => singularity For some reason ours are lowercase --- conf/utd_ganymede.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/utd_ganymede.config b/conf/utd_ganymede.config index a183861..8b72448 100644 --- a/conf/utd_ganymede.config +++ b/conf/utd_ganymede.config @@ -12,7 +12,7 @@ singularity { } process { - beforeScript = 'module load Singularity/2.4.5' + beforeScript = 'module load singularity' executor = 'slurm' queue = 'genomics' }