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Pbs draft add in? #40

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ca4cd85
pbs yaml
Aug 21, 2020
84ce076
updated pbs submit
halexand Aug 21, 2020
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82 changes: 82 additions & 0 deletions cluster-pbs.yaml
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Original file line number Diff line number Diff line change
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__default__:
account: haleysh
command_options:
slurm:
account: --account={}
command: sbatch --parsable --qos=unlim
key_mapping: null
mem: --mem={}gb
name: --job-name={}
nodes: -N {}
queue: --partition={}
threads: -n {}
time: --time={}
pbs:
command: sbatch
key_mapping: null
mem: -l vmem={}gb
name: -N {}
nodes: -l nodes={}
queue: –partition={}
threads: -l ppn={}
time: -l walltime={}
cpupertask: 18
mem: 180
nodes: 1
queue: scavenger
system: slurm
tasks: 1
time: 1400
fastqc:
account: haleysh
cpupertask: 5
mem: 1
queue: scavenger
tasks: 1
time: 720
fastqc_trimmed:
account: haleysh
cpupertask: 5
mem: 1
queue: scavenger
tasks: 1
time: 720
required:
accountname: haleysh
defaultqueue: scavenger
maxcores: 1
maxcpuspertask: 18
maxmemory: 180
maxtasks: 1
transabyssmerge:
account: haleysh
cpupertask: 18
mem: 180
nodes: 1
queue: scavenger
tasks: 1
time: 10000
trimmomatic:
account: haleysh
cpupertask: 5
mem: 48
nodes: 1
queue: scavenger
tasks: 1
time: 1400
trinity:
account: haleysh
cpupertask: 20
mem: 500
nodes: 1
queue: bigmem
tasks: 1
time: 10000
velvet:
account: haleysh
cpupertask: 18
mem: 180
nodes: 1
queue: scavenger
tasks: 1
time: 10000
2 changes: 2 additions & 0 deletions snake-submit-pbs.sh
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snakemake --rerun-incomplete --jobs 50 --use-conda --cluster-config cluster-pbs.yaml --cluster "qsub -N {rule}.{wildcards} -l vmem={cluster.mem}gb,walltime={cluster.time},nodes={cluster.nodes}:ppn={cluster.cpupertask}"