RunSnake.sh 497 Bytes
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#!/bin/bash
export PYTHONPATH=''
source /usr/local/genome/Anaconda2-5.1.0/etc/profile.d/conda.sh
conda activate snakemake-5.7.4

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mkdir -p ./.log/out/ ./.log/err/

snakemake \
--snakefile $1 \
--jobscript jobscript.sh \
--cluster-config cluster.json \
--cluster "qsub -V -cwd -N {rule} -o {cluster.out} -e {cluster.err} -q {cluster.queue} -pe thread {threads} {cluster.cluster}" \
--keep-going \
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--restart-times 5 \
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--jobs 80 \
--wait-for-files \
--latency-wait 150 \
--verbose \
--printshellcmds