Mercurial > repos > fubar > egapx_runner
comparison ui/assets/config/executor/ncbi-sge.config @ 0:d9c5c5b87fec draft
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
| author | fubar |
|---|---|
| date | Sat, 03 Aug 2024 11:16:53 +0000 |
| parents | |
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| -1:000000000000 | 0:d9c5c5b87fec |
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| 1 // This is an example of SGE executor configuration | |
| 2 // It is specific for internal NCBI use, you need to supply -P and -A parameters specific to your HPC | |
| 3 // account. Keep -V, maybe adjust osverfull parameters (set to use Alma Linux 8) | |
| 4 // This configuration uses binaries setup directly on network accessible drive. We currently don't support | |
| 5 // such configurations for third party, use docker or singularity for this. Uncomment corresponding line below | |
| 6 //docker.enabled = true | |
| 7 //singularity.enabled = true | |
| 8 process { | |
| 9 executor = 'sge' | |
| 10 clusterOptions = "-m n -V -P progressive -w n -A annotations-euk -l express=TRUE,h_vmem=INFINITY,m_core=12,osverfull='8*'" | |
| 11 } | |
| 12 env.GP_HOME="/netmnt/vast01/egapx/bin/" | |
| 13 env.PATH = "/netmnt/vast01/egapx/bin:/netmnt/vast01/egapx/bin/gp:/netmnt/vast01/egapx/bin/third-party/STAR/bin/Linux_x86_64:\$PATH" | |
| 14 process { | |
| 15 memory = 60.GB | |
| 16 time = 3.h | |
| 17 | |
| 18 withLabel: 'big_job' { | |
| 19 memory = 120.GB | |
| 20 } | |
| 21 | |
| 22 withLabel: 'huge_job' { | |
| 23 memory = 200.GB | |
| 24 } | |
| 25 | |
| 26 withLabel: 'long_job' { | |
| 27 time = 6.h | |
| 28 } | |
| 29 } |