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Merge pull request #285 from bbartholdy/master
Add ALICE cluster to profiles
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commit
8e554cd43c
5 changed files with 70 additions and 0 deletions
1
.github/workflows/main.yml
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1
.github/workflows/main.yml
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@ -18,6 +18,7 @@ jobs:
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matrix:
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profile:
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- 'abims'
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- 'alice'
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- 'aws_tower'
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- 'awsbatch'
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- 'bi'
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@ -91,6 +91,7 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs
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Currently documentation is available for the following systems:
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* [ABIMS](docs/abims.md)
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* [ALICE](docs/alice.md)
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* [AWSBATCH](docs/awsbatch.md)
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* [AWS_TOWER](docs/aws_tower.md)
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* [BIGPURPLE](docs/bigpurple.md)
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39
conf/alice.config
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39
conf/alice.config
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params {
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config_profile_name = 'ALICE'
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config_profile_description = 'Profile for use on Academic Leiden Interdisciplinary Cluster Environment (ALICE).'
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config_profile_contact = 'Bjorn Peare Bartholdy (@osteobjorn)'
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config_profile_url = 'https://wiki.alice.universiteitleiden.nl/'
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max_cpus = 24
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max_memory = 240.GB
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max_time = 168.h
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}
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process {
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executor = 'slurm'
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queue = { task.time < 3.h ? 'cpu-short' : task.time < 24.h ? 'cpu-medium' : 'cpu-long' }
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}
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singularity {
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enabled = true
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autoMounts = true
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}
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// Preform work directory cleanup after a successful run
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cleanup = true
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// Profile to deactivate automatic cleanup of work directory after a successful run. Overwrites cleanup option.
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profiles {
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mem {
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params {
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max_cpus = 24
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max_memory = 2.TB
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max_time = 336.h
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}
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process {
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queue = 'mem'
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}
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}
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debug {
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cleanup = false
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}
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}
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28
docs/alice.md
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28
docs/alice.md
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@ -0,0 +1,28 @@
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# nf-core/configs: Academic Leiden Interdisciplinary Cluster Environment (ALICE), Leiden University Configuration
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> **NB:** You will need an [account](https://wiki.alice.universiteitleiden.nl/index.php?title=Getting_an_account) to use the HPC cluster to run the pipeline.
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The profile is configured to run with Singularity version 3.6.1-Go-1.14 and needs to be loaded as a module.
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Before running the pipeline you will need to load Java and Nextflow. You can do this by including the commands below in your SLURM/sbatch script:
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```bash
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## Load Java and Nextflow environment modules
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module load Singularity/3.6.1-Go-1.14
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module load Nextflow/21.03.0
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module load Java/11.0.2
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```
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We also highly recommend specifying a location of a cache directory to store singularity images (so you re-use them across runs, and not pull each time), by specifying the location with the `$NXF_SINGULARITY_CACHE_DIR` bash environment variable in your `.bash_profile` or `.bashrc`.
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All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
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The config contains a `cleanup` command that removes the `work/` directory automatically once the pipeline has completeed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space.
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This configuration will automatically choose the correct SLURM queue (short,medium,long) depending on the time required by each process. If there are
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high memory requirements (>240GB), e.g. using MALT, use the 'mem' profile:
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```bash
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run nextflow nf-core/eager -p alice,mem
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```
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> **NB:** Nextflow will need to submit the jobs via SLURM to the HPC cluster and as such the commands above will have to be submitted from one of the login nodes.
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@ -11,6 +11,7 @@
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//Please use a new line per include Config section to allow easier linting/parsing. Thank you.
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profiles {
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abims { includeConfig "${params.custom_config_base}/conf/abims.config" }
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alice { includeConfig "${params.custom_config_base}/conf/alice.config" }
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aws_tower { includeConfig "${params.custom_config_base}/conf/aws_tower.config" }
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awsbatch { includeConfig "${params.custom_config_base}/conf/awsbatch.config" }
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bi { includeConfig "${params.custom_config_base}/conf/bi.config" }
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