Commit f7bc787b authored by Beatrice Tan's avatar Beatrice Tan
Browse files

Update run_pipeline_cluster.sh to prevent the need to specify config an snakefile location.

parent ae28e193
...@@ -10,16 +10,16 @@ ...@@ -10,16 +10,16 @@
#$ -M b.f.tan@lumc.nl #$ -M b.f.tan@lumc.nl
##Create or update conda environment and activate it ##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 && source activate CNAprioritization &&
snakemake --unlock && snakemake --unlock &&
##Run snakemake ##Run snakemake
snakemake -p \ snakemake -p \
--configfile /home/bftan/PrioritizationCNAs/config.yaml \ --configfile config.yaml \
--snakefile /home/bftan/PrioritizationCNAs/Snakefile \ --snakefile Snakefile \
--latency-wait 90 \ --latency-wait 90 \
--jobs 1 \ --jobs 1 \
--max-jobs-per-second 10 \ --max-jobs-per-second 10 \
--restart-times 3 \ --restart-times 3 \
--use-conda \ --use-conda \
--conda-prefix /home/bftan/.conda --conda-prefix ~/.conda
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