Commit e1a25923 authored by Midoux Cedric's avatar Midoux Cedric
Browse files

snakemake toolbox

parent 0ec8551b
.log/
.snakemake/
DATA/
work/
report/
#!/bin/bash
export PYTHONPATH=''
source activate snakemake-5.4.5
mkdir -p ./.log/out/ ./.log/err/
snakemake \
--snakefile $1 \
--jobscript jobscript.sh \
--cluster-config cluster.json \
--cluster "qsub -V -cwd -R y -N {rule} -o {cluster.out} -e {cluster.err} -q {cluster.queue} -pe thread {threads} {cluster.cluster}" \
--keep-going \
--jobs 80 \
--use-conda \
--conda-prefix /projet/maiage/save/cmidoux/environments/ \
--wait-for-files \
--latency-wait 150 \
--use-conda \
--verbose \
--printshellcmds
#!/bin/bash
export PYTHONPATH=''
source activate snakemake-5.4.5
mkdir -p report/
snakemake \
--snakefile $1 \
--dag \
| dot -Tpdf > ./report/`basename $1 .smk`_graph.pdf
#!/bin/bash
export PYTHONPATH=''
source activate snakemake-5.4.5
snakemake \
--snakefile $1 \
--jobscript jobscript.sh \
--cluster-config cluster.json \
--dryrun \
--forceall \
--printshellcmds \
--verbose
#!/bin/bash
export PYTHONPATH=''
source activate snakemake-5.4.5
snakemake \
--snakefile $1 \
--jobscript jobscript.sh \
--cluster-config cluster.json \
--dryrun \
--printshellcmds \
--verbose
#!/bin/bash
export PYTHONPATH=''
source activate snakemake-5.4.5
mkdir -p report/
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" : "maiage.q",
"cluster" : ""
},
"kaiju" :
{
"queue" : "highmem.q,maiage.q",
"cluster" : "-l h_vmem={MEM}G"
},
"interleave" :
{
"queue" : "highmem.q,maiage.q",
"cluster" : "-l h_vmem={MEM}G"
},
"khmer" :
{
"queue" : "highmem.q,maiage.q",
"cluster" : "-l h_vmem={MEM}G"
},
"megahit" :
{
"queue" : "highmem.q,maiage.q",
"cluster" : "-l h_vmem={MEM}G"
},
"metaspades" :
{
"queue" : "highmem.q,maiage.q",
"cluster" : "-l h_vmem={MEM}G"
},
"diamond" :
{
"queue" : "highmem.q,maiage.q",
"cluster" : "-l h_vmem={MEM}G"
}
}
{
"SAMPLES": ["a", "b", "c"],
"NORMALIZATION": false,
"SORTMERNA": false,
"ASSEMBLER": "metaspades",
"CONTIGS_LEN": 1000
}
#!/bin/sh
# properties = {properties}
export PYTHONPATH=''
source activate snakemake-5.4.5
{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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