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Merge pull request #216 from asafpr/master

Added JAX conf
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Asaf Peer 2021-03-24 03:31:14 -04:00 committed by GitHub
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5 changed files with 32 additions and 1 deletions

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@ -16,7 +16,7 @@ jobs:
needs: test_all_profiles
strategy:
matrix:
profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
steps:
- uses: actions/checkout@v1
- name: Install Nextflow

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@ -113,6 +113,7 @@ Currently documentation is available for the following systems:
* [GOOGLE](docs/google.md)
* [HEBBE](docs/hebbe.md)
* [ICR_DAVROS](docs/icr_davros.md)
* [JAX](docs/jax.md)
* [KRAKEN](docs/kraken.md)
* [MPCDF](docs/mpcdf.md)
* [MUNIN](docs/munin.md)

21
conf/jax.config Normal file
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@ -0,0 +1,21 @@
params {
config_profile_description = 'The Jackson Laboratory Sumner HPC profile provided by nf-core/configs.'
config_profile_contact = 'Asaf Peer (@peera)'
config_profile_url = 'https://jacksonlaboratory.sharepoint.com/sites/ResearchIT/SitePages/Welcome-to-Sumner.aspx'
}
executor.$slurm.queueSize = 250
process {
executor = "slurm"
queue = "compute"
clusterOptions = {task.time < 72.h ? '-q batch' : '-q long'}
module = "slurm"
beforeScript = 'module load singularity'
}
singularity.enabled = true
singularity.autoMounts = true
params {
max_memory = 768.GB
max_cpus = 70
max_time = 336.h
}

8
docs/jax.md Normal file
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@ -0,0 +1,8 @@
# nf-core/configs: JAX Configuration
All nf-core pipelines have been successfully configured for use on the JAX Sumner cluster at The Jackson Laboratory.
To use, run the pipeline with `-profile jax`. This will download and launch the [`jax.config`](../conf/jax.config) which has been pre-configured with a setup suitable for JAX Sumner 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 and slurm will be used as well.
>NB: You will need an account to use the HPC cluster JAX in order to run the pipeline. If in doubt contact IT.
>NB: Nextflow should not be executed on the login nodes. If in doubt contact IT.

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@ -46,6 +46,7 @@ profiles {
uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" }
uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" }
jax { includeConfig "${params.custom_config_base}/conf/jax.config" }
}
// If user hostnames contain one of these substring and they are