Commit f4f0bd06 authored by Jan Hoeckesfeld's avatar Jan Hoeckesfeld
Browse files

introducing attempts

parent 7491e4d7
......@@ -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
......@@ -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 = '15G',
cpus = lambda wildcards, attempt: str(2*attempt),
mem = '10G',
gpus = '0',
walltime = '00:30:00'
walltime = lambda wildcards, attempt: '0' + str(attempt) + ':00:00'
singularity:
'singularity_container/ckmertools_iterset.sif'
#'docker://phspo/ckmertools:iterationset-tests'
......
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