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comparison resfinder/scripts/wdl/computerome.conf @ 0:55051a9bc58d draft default tip

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author dcouvin
date Mon, 10 Jan 2022 20:06:07 +0000
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1 # TORQUE as a backend for Cromwell on Computerome
2
3 # Here is where you can define the backend providers that Cromwell understands.
4 # The default is a local provider.
5 # To add additional backend providers, you should copy paste additional backends
6 # of interest that you can find in the cromwell.example.backends folder
7 # folder at https://www.github.com/broadinstitute/cromwell
8 # Other backend providers include SGE, SLURM, Docker, udocker, Singularity. etc.
9 # Don't forget you will need to customize them for your particular use case.
10
11 backend {
12
13 # Override the default backend.
14 default = TORQUE
15
16 # The list of providers.
17 providers {
18
19 TORQUE {
20
21 # The actor that runs the backend.
22 actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
23
24 # The backend custom configuration.
25 config {
26
27 # Number of concurrent jobs allowed
28 concurrent-job-limit = 500
29
30 # The list of possible runtime custom attributes.
31 runtime-attributes = """
32 String walltime = "1:00:00"
33 Int cpu = 1
34 Float memory_mb = 2048.0
35 String queue = "cge"
36 """
37
38 submit = "qsub -W group_list=${queue} -A ${queue} -N ${job_name} -lwalltime=${walltime},nodes=1:ppn=${cpu},mem=${ceil(memory_mb)}mb -d ${cwd} -o ${out} -e ${err} ${script}"
39
40 kill = "qdel ${job_id}"
41 check-alive = "qstat ${job_id}"
42 job-id-regex = "(\\d+)"
43 }
44
45 }
46
47 }
48
49 }