Merge pull request #135 from Emiller88/utd

feat: add initial ganymede config

.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

README.md

@@ -118,6 +118,7 @@ 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`

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'
+  executor = 'slurm'
+  queue = 'genomics'
+}
+
+params {
+  max_memory = 32.GB
+  max_cpus = 16
+  max_time = 48.h
+}

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.

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']
   ]
 }