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Merge pull request #346 from sagc-bioinformatics/sahmri
Added SAHMRI profile
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commit
962d86d604
4 changed files with 54 additions and 0 deletions
1
.github/workflows/main.yml
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1
.github/workflows/main.yml
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@ -76,6 +76,7 @@ jobs:
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- 'phoenix'
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- 'phoenix'
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- 'prince'
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- 'prince'
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- 'rosalind'
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- 'rosalind'
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- 'sahmri'
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- 'sanger'
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- 'sanger'
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- 'seg_globe'
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- 'seg_globe'
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- 'uct_hpc'
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- 'uct_hpc'
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34
conf/sahmri.config
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34
conf/sahmri.config
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@ -0,0 +1,34 @@
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params {
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config_profile_description = 'South Australian Health and Medical Research Institute (SAHMRI) HPC cluster profile.'
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config_profile_contact = 'Nathan Watson-Haigh (nathan.watson-haigh@sahmri.com)'
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config_profile_url = "https://sahmri.org.au"
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max_memory = 375.GB
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max_cpus = 32
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max_time = 14.d
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igenomes_base = '/cancer/storage/shared/igenomes/references/'
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}
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process {
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executor = 'slurm'
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queue = 'sahmri_prod_hpc,sahmri_cancer_hpc'
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maxRetries = 2
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cpus = { check_max( 2 * task.attempt, 'cpus') }
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memory = { check_max( 1.GB * task.attempt, 'memory') }
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time = { check_max( 10.m * task.attempt, 'time') }
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}
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executor {
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queueSize = 50
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submitRateLimit = '10 sec'
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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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beforeScript = 'export PATH=/apps/opt/singularity/latest/bin:${PATH}'
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cacheDir = '/cancer/storage/shared/simg'
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}
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cleanup = true
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profiles {
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debug {
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cleanup = false
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}
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}
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18
docs/sahmri.md
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18
docs/sahmri.md
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# nf-core/configs: SAHMRI HPC Configuration
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All nf-core pipelines have been successfully configured for use on the HPC cluster at [SAHMRI](https://sahmri.org.au/).
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To use, run the pipeline with `-profile sahmri`. This will download and launch the [`sahmri.config`](../conf/sahmri.config) which has been pre-configured
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with a setup suitable for the SAHMRI HPC cluster. Using this profile, either a docker image containing all of the required software will be downloaded,
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and converted to a Singularity image or a Singularity image downloaded directly before execution of the pipeline.
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The latest version of Nextflow is not installed by default on the SAHMRI HPC cluster. You will need to install it into a directory you have write access to.
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Follow these instructions from the Nextflow documentation.
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- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
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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
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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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> NB: You will need an account to use the SAHMRI HPC cluster in order to run the pipeline. If in doubt contact the ICT Service Desk.
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> NB: Nextflow will need to submit the jobs via SLURM to the SAHMRI HPC cluster and as such the commands above will have to be executed on the login
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node. If in doubt contact ICT.
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@ -57,6 +57,7 @@ profiles {
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phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" }
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phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" }
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prince { includeConfig "${params.custom_config_base}/conf/prince.config" }
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prince { includeConfig "${params.custom_config_base}/conf/prince.config" }
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rosalind { includeConfig "${params.custom_config_base}/conf/rosalind.config" }
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rosalind { includeConfig "${params.custom_config_base}/conf/rosalind.config" }
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sahmri { includeConfig "${params.custom_config_base}/conf/sahmri.config" }
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sanger { includeConfig "${params.custom_config_base}/conf/sanger.config"}
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sanger { includeConfig "${params.custom_config_base}/conf/sanger.config"}
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seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
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seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
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uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }
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uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }
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