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Merge pull request #245 from ikeller/unibe_ibu

Unibe ibu
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Phil Ewels 2021-11-19 00:56:25 +01:00 committed by GitHub
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@ -62,6 +62,7 @@ jobs:
- 'sanger'
- 'seg_globe'
- 'uct_hpc'
- 'unibe_ibu'
- 'uppmax'
- 'utd_ganymede'
- 'utd_sysbio'

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@ -125,6 +125,7 @@ Currently documentation is available for the following systems:
* [SANGER](docs/sanger.md)
* [SEG_GLOBE](docs/seg_globe.md)
* [UCT_HPC](docs/uct_hpc.md)
* [UNIBE_IBU](docs/unibe_ibu.md)
* [UPPMAX](docs/uppmax.md)
* [UTD_GANYMEDE](docs/utd_ganymede.md)
* [UTD_SYSBIO](docs/utd_sysbio.md)

23
conf/unibe_ibu.config Normal file
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params {
config_profile_description = "University of Bern, Interfaculty Bioinformatics Unit cluster profile"
config_profile_contact = "irene.keller@dbmr.unibe.ch; info@bioinformatics.unibe.ch"
config_profile_url = "https://www.bioinformatics.unibe.ch/"
max_memory = 500.GB
max_cpus = 128
max_time = 240.h
}
process {
executor = "slurm"
maxRetries = 2
beforeScript = 'mkdir -p ./tmp/ && export TMPDIR=./tmp/'
}
executor {
queueSize = 30
}
singularity {
enabled = true
autoMounts = true
}

5
docs/unibe_ibu.md Normal file
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# nf-core/configs: UNIBE_IBU Configuration
Configuration file to run nf-core pipelines on the cluster of the [Interfaculty Bioinformatics Unit](https://www.bioinformatics.unibe.ch/) of the University of Bern.
To use, run the pipeline with `-profile unibe_ibu`. This will download and launch the profile.config which has been pre-configured with a setup suitable for the IBU 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. **This requires a local installation of singularity**. It is easiest to submit the pipeline from a compute node. Once the image is cached, you can also submit from the login node.

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@ -56,6 +56,7 @@ profiles {
sanger { includeConfig "${params.custom_config_base}/conf/sanger.config"}
seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }
unibe_ibu { includeConfig "${params.custom_config_base}/conf/unibe_ibu.config" }
uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" }
utd_sysbio { includeConfig "${params.custom_config_base}/conf/utd_sysbio.config" }