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Jan Hoeckesfeld
Snakemake Ngs Spa Typing
Commits
f4f0bd06
Commit
f4f0bd06
authored
Feb 07, 2021
by
Jan Hoeckesfeld
Browse files
introducing attempts
parent
7491e4d7
Changes
2
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clusterExecution.sh
View file @
f4f0bd06
...
...
@@ -4,6 +4,8 @@ module load Singularity/3.5.2
module load Miniconda/3_snakemake
module load Snakemake/5.10.0
export
SINGULARITY_CACHEDIR
=
/tmp/.singularity-
$(
id
-u
)
while
getopts
"p:j:"
opt
do
case
$opt
in
...
...
@@ -22,5 +24,5 @@ mkdir -p clusterLogs
type
snakemake
>
/dev/null 2>&1
||
{
echo
>
&2
"I require snakemake but it's not installed or added to your path. Aborting..."
;
exit
1
;
}
snakemake
--jobs
$maxNrOfConcurrentJobs
--use-singularity
--use-conda
--reason
--jobscript
cluster/jobscript.sh
--cluster
"qsub -e clusterLogs/{rule}.{wildcards}.{jobid}.errors -o clusterLogs/{rule}.{wildcards}.{jobid}.output -A
${
projectID
}
-l select=1:ncpus={params.cpus}:ngpus={params.gpus}:mem={params.mem} -l walltime={params.walltime}"
snakemake
--jobs
$maxNrOfConcurrentJobs
--use-singularity
--use-conda
--reason
--jobscript
cluster/jobscript.sh
--cluster
"qsub -e clusterLogs/{rule}.{wildcards}.{jobid}.errors -o clusterLogs/{rule}.{wildcards}.{jobid}.output -A
${
projectID
}
-l select=1:ncpus={params.cpus}:ngpus={params.gpus}:mem={params.mem} -l walltime={params.walltime}"
--restart-times
3
--envvars
SINGULARITY_CACHEDIR
rules/probabilistic.smk
View file @
f4f0bd06
...
...
@@ -81,10 +81,10 @@ rule calcLikelihoods:
deviationCutoff = (lambda wildcards,input : round(config['deviationCutoff']*extractCoverageEstimateFile(input.kmerCoverageEstimate,config))),
itersetType = lambda wildcards: wildcards.iterset,
#cluster exectuion
cpus =
'8'
,
mem = '1
5
G',
cpus =
lambda wildcards, attempt: str(2*attempt)
,
mem = '1
0
G',
gpus = '0',
walltime =
'00:3
0:00'
walltime =
lambda wildcards, attempt: '0' + str(attempt) + ':0
0:00'
singularity:
'singularity_container/ckmertools_iterset.sif'
#'docker://phspo/ckmertools:iterationset-tests'
...
...
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