Merge branch 'nf-core:master' into sbc_sharc
Lewis Quayle
2 years ago
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GitHub
commit
755862fc61
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params {
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config_profile_description = 'University of Hawaii at Manoa'
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config_profile_url = 'http://www.hawaii.edu/its/ci/'
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config_profile_contact = 'Cedric Arisdakessian'
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max_memory = 400.GB
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max_cpus = 96
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max_time = 72.h
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}
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process {
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executor = 'slurm'
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queue = 'shared,exclusive,kill-shared,kill-exclusive'
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module = 'tools/Singularity'
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}
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singularity {
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enabled = true
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cacheDir = "$HOME/.singularity_images_cache"
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autoMounts = true
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}
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params {
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config_profile_description = 'Telethon Institute of Genetic and Medicine (TIGEM) provided by nf-core/configs.'
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config_profile_contact = 'Giuseppe Martone (@giusmar)'
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config_profile_url = 'https://github.com/giusmar'
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}
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process.executor = 'slurm'
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google.zone = 'europe-west1'
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singularity {
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enabled = true
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autoMounts = true
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cacheDir = 'work/singularity'
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}
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# nf-core/configs Mana (at University of Hawaii at Manoa) Configuration
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To use, run the pipeline with `-profile mana`. It will use the following parameters for Mana (UHM HPCC):
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- Load singularity and use it as default container technology
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- Setup a container cache directory in your home (~/.singularity_images_cache)
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- Select appropriate queues (currently: `shared,exclusive,kill-shared,kill-exclusive`)
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- Set the maximum available resources (available in 09/02/2022):
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- CPUs: 96
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- Memory: 400.GB
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- Time: 72.h
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## Pre-requisites
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In order to run a nf-core pipeline on Mana, you will need to setup nextflow in your environment.
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At the moment, nextflow is not available as a module (but might be in the future).
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### Install nextflow in a conda environment
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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):
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```bash
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# Request an interactive sandbox node for 30 min
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srun --pty -t 30 -p sandbox /bin/bash
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```
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To setup nextflow on your account, follow these steps.
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```bash
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# Load the latest anaconda3 module
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module load lang/Anaconda3/2022.05
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# Initialize environment
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. $(conda info --base)/etc/profile.d/conda.sh
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# Install nextflow (here in base environment, but you can create a new one if you'd like)
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conda install -c bioconda nextflow
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```
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If you want these settings to be persistent, you can add the first 2 commands in your .bash_profile file like this:
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```bash
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echo "module load lang/Anaconda3/2022.05" >> ~/.bash_profile
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echo "$(conda info --base)/etc/profile.d/conda.sh" >> ~/.bash_profile
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```
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# nf-core/configs: TIGEM configuration
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To use, run the pipeline with `-profile tigem`. This will download and launch the tigem.config which has been pre-configured with a setup suitable for the TIGEM personal biocluster.
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---
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This configuration profile can be used on TIGEM clusters, with the pre-installed SLURM job scheduling system. An additional parameter is `google.zone` to allow downloading data from GCP for a specific time zone. It should not interfere with any local or other AWS configuration.
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