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memory test

This commit is contained in:
Barry digby 2021-04-29 14:24:57 +01:00
parent aeb0346cce
commit 24a4119e43
2 changed files with 25 additions and 8 deletions

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@ -1,7 +1,7 @@
//Profile config names for nf-core/configs
params {
config_profile_description = 'National University of Ireland, Galway SLURM cluster profile provided by nf-core/configs'
config_profile_description = 'National University of Ireland, Galway Lugh cluster profile provided by nf-core/configs'
config_profile_contact = 'Barry Digby (@BarryDigby)'
config_profile_url = 'https://github.com/nf-core/configs/blob/master/docs/nuig.md'
}
@ -9,22 +9,24 @@ params {
singularity {
enabled = true
autoMounts = true
cacheDir = '/data/bdigby/containers'
cacheDir = '/data/containers'
}
process {
beforeScript = 'module load singularity/3.4.1'
beforeScript = """
module load EasyBuild/3.4.1
module load Java/1.8.0_144
module load singularity/3.4.1
"""
.stripIndent()
containerOptions = '-B /data/'
executor = 'slurm'
queue = { task.cpus > 8 ? 'highmem' : 'normal' }
withName: '*' { memory = null }
}
/*
NUIG SLURM is not configured to use the memory parameter, please do not include
However, the highmem queue has 128GB memory and the normal queue has 64GB.
*/
params {
max_time = '120.d'
max_memory = '64.GB'
max_cpus = '16'
}

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@ -0,0 +1,15 @@
# nf-core/configs: National University of Ireland, Galway (Lugh) Configuration
All nf-core pipelines have been successfully configured for use on Lugh at the [National University of Ireland, Galway](http://maths.nuigalway.ie/biocluster/).
To use, run the pipeline with `-profile nuig`. This will download and launch the [`nuig.config`](../conf/nuig.config) which has been pre-configured with a setup suitable for Lugh. 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.
## Running nextflow on Lugh
Before running a pipeline you will need a working version of nextflow. Please follow the install instructions below:
- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
* Install Nextflow edge: download the latest source code from Nextflow GitHub [releases](https://github.com/nextflow-io/nextflow/releases). Unpack source code, compile using `make`, add `nextflow` to your `$PATH` when complete.
One quirk of Lugh that will produce errors unless addressed: Lugh is not configured to take `memory` parameters in pipelines. This means you will have to make a fork of the pipeline, comment out (`//`) all instances of memory in config files (`nextflow.config`, `base.config`, `test.config` ) AND do away with any instances of `toGiga()` in the pipeline.