Mercurial > repos > fubar > egapx_runner
diff ui/assets/config/executor/slurm.config @ 0:d9c5c5b87fec draft
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
author | fubar |
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date | Sat, 03 Aug 2024 11:16:53 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ui/assets/config/executor/slurm.config Sat Aug 03 11:16:53 2024 +0000 @@ -0,0 +1,37 @@ +// Config for typical SLURM cluster +// Adjust the parameters for your cluster - queue name, temp dir, etc. +// Use your temp space instead of /data/$USER in the following config + +singularity { + enabled = true + autoMounts = true + cacheDir = "/data/$USER/singularity" + envWhitelist='https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOB_ID,SINGULARITY_BINDPATH' +} + +env { + SINGULARITY_CACHEDIR="/data/$USER/singularity" + SINGULARITY_TMPDIR="/data/$USER/tmp" +} + +process { + executor = 'slurm' + // Set other parameters specific to your cluser here + // maxRetries = 1 + // queue = 'norm' + // queueSize = 200 + // pollInterval = '2 min' + // queueStatInterval = '5 min' + // submitRateLimit = '6/1min' + // retry.maxAttempts = 1 + + // clusterOptions = ' --gres=lscratch:200 ' + + // scratch = '/lscratch/$SLURM_JOB_ID' + // with the default stageIn and stageOut settings using scratch can + // result in humungous work folders + // see https://github.com/nextflow-io/nextflow/issues/961 and + // https://www.nextflow.io/docs/latest/process.html?highlight=stageinmode + //stageInMode = 'symlink' + //stageOutMode = 'rsync' +}