Merge pull request #421 from Puumanamana/master

University of Hawaii at Manoa's HPCC config

.github/workflows/main.yml

@@ -69,6 +69,7 @@ jobs:
           - "jax"
           - "ku_sund_dangpu"
           - "lugh"
+          - "mana"
           - "marvin"
           - "medair"
           - "mjolnir_globe"

README.md

@@ -125,6 +125,7 @@ Currently documentation is available for the following systems:
 - [KU SUND DANGPU](docs/ku_sund_dangpu.md)
 - [LUGH](docs/lugh.md)
 - [MAESTRO](docs/maestro.md)
+- [Mana](docs/mana.md)
 - [MARVIN](docs/marvin.md)
 - [MEDAIR](docs/medair.md)
 - [MJOLNIR_GLOBE](docs/mjolnir_globe.md)

conf/mana.config

@@ -0,0 +1,21 @@
+params {
+  config_profile_description = 'University of Hawaii at Manoa'
+  config_profile_url = 'http://www.hawaii.edu/its/ci/'
+  config_profile_contact = 'Cedric Arisdakessian'
+
+  max_memory = 400.GB
+  max_cpus = 96
+  max_time = 72.h
+}
+
+process {
+  executor = 'slurm'
+  queue = 'shared,exclusive,kill-shared,kill-exclusive'
+  module = 'tools/Singularity'
+}
+
+singularity {
+  enabled = true
+  cacheDir = "$HOME/.singularity_images_cache"
+  autoMounts = true
+}

docs/mana.md

@@ -0,0 +1,45 @@
+# nf-core/configs Mana (at University of Hawaii at Manoa) Configuration
+
+To use, run the pipeline with `-profile mana`. It will use the following parameters for Mana (UHM HPCC):
+
+- Load singularity and use it as default container technology
+- Setup a container cache directory in your home (~/.singularity_images_cache)
+- Select appropriate queues (currently: `shared,exclusive,kill-shared,kill-exclusive`)
+- Set the maximum available resources (available in 09/02/2022):
+  - CPUs: 96
+  - Memory: 400.GB
+  - Time: 72.h
+
+## Pre-requisites
+
+In order to run a nf-core pipeline on Mana, you will need to setup nextflow in your environment.
+At the moment, nextflow is not available as a module (but might be in the future).
+
+### Install nextflow in a conda environment
+
+Before we start, we will need to work on an interactive node (currently, mana doesn't let you execute any program in the login node):
+
+```bash
+# Request an interactive sandbox node for 30 min
+srun --pty -t 30 -p sandbox /bin/bash
+```
+
+To setup nextflow on your account, follow these steps.
+
+```bash
+# Load the latest anaconda3 module
+module load lang/Anaconda3/2022.05
+
+# Initialize environment
+. $(conda info --base)/etc/profile.d/conda.sh
+
+# Install nextflow (here in base environment, but you can create a new one if you'd like)
+conda install -c bioconda nextflow
+```
+
+If you want these settings to be persistent, you can add the first 2 commands in your .bash_profile file like this:
+
+```bash
+echo "module load lang/Anaconda3/2022.05" >> ~/.bash_profile
+echo "$(conda info --base)/etc/profile.d/conda.sh" >> ~/.bash_profile
+```

nfcore_custom.config

@@ -52,6 +52,7 @@ profiles {
   ku_sund_dangpu {includeConfig "${params.custom_config_base}/conf/ku_sund_dangpu.config"}
   lugh         { includeConfig "${params.custom_config_base}/conf/lugh.config" }
   maestro      { includeConfig "${params.custom_config_base}/conf/maestro.config" }
+  mana         { includeConfig "${params.custom_config_base}/conf/mana.config" }
   marvin       { includeConfig "${params.custom_config_base}/conf/marvin.config" }
   medair       { includeConfig "${params.custom_config_base}/conf/medair.config" }
   mjolnir_globe { includeConfig "${params.custom_config_base}/conf/mjolnir_globe.config" }