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nuig confg (lugh)
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6 changed files with 24 additions and 21 deletions
2
.github/workflows/main.yml
vendored
2
.github/workflows/main.yml
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@ -16,7 +16,7 @@ jobs:
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needs: test_all_profiles
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strategy:
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matrix:
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profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'biohpc_gen', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'mpcdf', 'munin', 'nuig', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
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profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'biohpc_gen', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'lugh', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
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steps:
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- uses: actions/checkout@v1
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- name: Install Nextflow
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@ -118,9 +118,9 @@ Currently documentation is available for the following systems:
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* [ICR_DAVROS](docs/icr_davros.md)
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* [JAX](docs/jax.md)
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* [KRAKEN](docs/kraken.md)
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* [LUGH](docs/lugh.md)
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* [MPCDF](docs/mpcdf.md)
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* [MUNIN](docs/munin.md)
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* [NUIG](docs/nuig.md)
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* [OIST](docs/oist.md)
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* [PASTEUR](docs/pasteur.md)
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* [PHOENIX](docs/phoenix.md)
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@ -3,7 +3,7 @@
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params {
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config_profile_description = 'National University of Ireland, Galway Lugh cluster profile provided by nf-core/configs'
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config_profile_contact = 'Barry Digby (@BarryDigby)'
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config_profile_url = 'https://github.com/nf-core/configs/blob/master/docs/nuig.md'
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config_profile_url = 'https://github.com/nf-core/configs/blob/master/docs/lugh.md'
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}
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singularity {
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@ -17,12 +17,12 @@ process {
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module load EasyBuild/3.4.1
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module load Java/1.8.0_144
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module load singularity/3.4.1
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ulimit -s unlimited
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"""
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.stripIndent()
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containerOptions = '-B /data/'
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executor = 'slurm'
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queue = { task.cpus > 8 ? 'highmem' : 'normal' }
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withName: '*' { memory = null }
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queue = { task.memory >= 64.GB || task.cpus > 16 ? 'highmem' : 'normal' }
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}
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params {
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18
docs/lugh.md
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18
docs/lugh.md
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@ -0,0 +1,18 @@
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# nf-core/configs: LUGH configuration
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To use the lugh configuration profile with your pipeline, add `-profile lugh` to your `nextflow run` command. Please take care to use the `-bg` flag or run the job on a compute node. DO NOT RUN ANALYSES ON THE HEAD NODE.
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The configuration file will load prerequisite modules for users, however it is entirely up to the user to have a functional version of nextflow installed in their path.
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Lugh has 3 queues:
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* `MSC`: compute0{1..3}, 16 cpus, 32GB memory (Please reserve for MSc students only)
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* `normal`: compute{10..29}, 16 cpus, 64GB memory.
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& `highmem`: compute0{4..9}, 32 cpus, 128GB memory.
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The configuration profile design is very simple. If your process exceeds 64GB memory or 16 cpus, it is sent to the `highmem` queue. Else, `normal`.
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Whilst I (@BarryDigby) am happy to help people set up their nextflow pipelines, please note that I am not the system administrator.
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### Container Cache
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Your workflow containers will be downloaded and stored at `/data/containers` which is accessible to all users.
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15
docs/nuig.md
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docs/nuig.md
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@ -1,15 +0,0 @@
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# nf-core/configs: National University of Ireland, Galway (Lugh) Configuration
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All nf-core pipelines have been successfully configured for use on Lugh at the [National University of Ireland, Galway](http://maths.nuigalway.ie/biocluster/).
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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.
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## Running nextflow on Lugh
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Before running a pipeline you will need a working version of nextflow. Please follow the install instructions below:
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- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
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* 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 `$PATH` when complete.
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One quirk of Lugh that will produce errors unless addressed: Lugh is not configured to take `memory` parameters in pipelines. This means you will have to make a fork of the pipeline, comment out (`//`) all instances of memory in config files (`nextflow.config`, `base.config`, `test.config` ) AND do away with any instances of `toGiga()` in the pipeline.
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@ -37,9 +37,9 @@ profiles {
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gis { includeConfig "${params.custom_config_base}/conf/gis.config" }
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hebbe { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
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kraken { includeConfig "${params.custom_config_base}/conf/kraken.config" }
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lugh { includeConfig "${params.custom_config_base}/conf/lugh.config"}
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mpcdf { includeConfig "${params.custom_config_base}/conf/mpcdf.config" }
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munin { includeConfig "${params.custom_config_base}/conf/munin.config" }
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nuig { includeConfig "${params.custom_config_base}/conf/nuig.config" }
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oist { includeConfig "${params.custom_config_base}/conf/oist.config" }
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pasteur { includeConfig "${params.custom_config_base}/conf/pasteur.config" }
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phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" }
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