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Commit 6a43f029 authored by Midoux Cedric's avatar Midoux Cedric
Browse files

snakemake tools

parent 2e94585a
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
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
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
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
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
{
"__default__" :
{
"out" : "./.log/out/",
"err" : "./.log/err/",
"queue" : "short.q",
"cluster" : ""
}
}
{
"THREADS": 8,
"MEM": 10
}
#!/bin/sh
# properties = {properties}
source /usr/local/genome/Anaconda3-5.1.0/envs/snakemake-5.2.0/snakemake-5.2.0_conda
{exec_job}
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
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