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Beatrice Tan
CNAprioritization
Commits
f7bc787b
Commit
f7bc787b
authored
Feb 01, 2018
by
Beatrice Tan
Browse files
Update run_pipeline_cluster.sh to prevent the need to specify config an snakefile location.
parent
ae28e193
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1
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run_pipeline_cluster.sh
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f7bc787b
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@@ -10,16 +10,16 @@
#$ -M b.f.tan@lumc.nl
##Create or update conda environment and activate it
#
conda-env update -n CNAprioritization -f envs/pipeline.yaml || conda-env create -n CNAprioritization -f envs/pipeline.yaml &&
conda-env update
-n
CNAprioritization
-f
envs/pipeline.yaml
||
conda-env create
-n
CNAprioritization
-f
envs/pipeline.yaml
&&
source
activate CNAprioritization
&&
snakemake
--unlock
&&
##Run snakemake
snakemake
-p
\
--configfile
/home/bftan/PrioritizationCNAs/
config.yaml
\
--snakefile
/home/bftan/PrioritizationCNAs/
Snakefile
\
--configfile
config.yaml
\
--snakefile
Snakefile
\
--latency-wait
90
\
--jobs
1
\
--max-jobs-per-second
10
\
--restart-times
3
\
--use-conda
\
--conda-prefix
/home/bftan
/.conda
--conda-prefix
~
/.conda
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