snakemake tools

RunSnake.sh

+mkdir -p ./.log/out/ ./.log/err/
+#PYTHONPATH=''
+source /usr/local/genome/Anaconda3-5.1.0/envs/snakemake-5.2.0/snakemake-5.2.0_conda
+
+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 \
+--jobs 80 \
+--wait-for-files \
+--latency-wait 150 \
+--verbose \
+--printshellcmds
+

RunSnake_graph.sh

+mkdir -p report/
+PYTHONPATH=''
+source /usr/local/genome/Anaconda3-5.1.0/envs/snakemake-5.2.0/snakemake-5.2.0_conda
+
+snakemake \
+--snakefile $1 \
+--dag \
+| dot -Tpdf > ./report/`basename $1 .smk`_graph.pdf

RunSnake_printshellcmds-forceall.sh

+PYTHONPATH=''
+source /usr/local/genome/Anaconda3-5.1.0/envs/snakemake-5.2.0/snakemake-5.2.0_conda
+
+snakemake \
+--snakefile $1 \
+--jobscript jobscript.sh \
+--cluster-config cluster.json \
+--dryrun \
+--forceall \
+--printshellcmds \
+--verbose

RunSnake_printshellcmds.sh

+PYTHONPATH=''
+source /usr/local/genome/Anaconda3-5.1.0/envs/snakemake-5.2.0/snakemake-5.2.0_conda
+
+snakemake \
+--snakefile $1 \
+--jobscript jobscript.sh \
+--cluster-config cluster.json \
+--dryrun \
+--printshellcmds \
+--verbose

RunSnake_report.sh

+mkdir -p report/
+PYTHONPATH=''
+source /usr/local/genome/Anaconda3-5.1.0/envs/snakemake-5.2.0/snakemake-5.2.0_conda
+
+snakemake \
+--snakefile $1 \
+--jobscript jobscript.sh \
+--cluster-config cluster.json \
+--report report/`basename $1 .smk`_report.html \
+--verbose

cluster.json

+{
+	"__default__" :
+	{
+		"out" : "./.log/out/",
+		"err" : "./.log/err/",
+		"queue" : "short.q",
+		"cluster" : ""
+	}
+}

config.json

+{
+	"THREADS": 8,
+	"MEM": 10
+}

jobscript.sh

+#!/bin/sh
+# properties = {properties}
+source /usr/local/genome/Anaconda3-5.1.0/envs/snakemake-5.2.0/snakemake-5.2.0_conda
+{exec_job}

qsubSnake.sh

+mkdir -p ./.log/out/ ./.log/err/
+qsub -V -cwd -o ./.log/out/ -e ./.log/err/ -q maiage.q,long.q -N `basename $1` RunSnake.sh $1