Kindly help me to resolve said issue
I run following command
snakemake -s Snakefile pretrained_predict -p --cores 1 --config mutations="data/bladder.txt" output_dir="output_bladder" trained_classifier="data/2020plus_10k.Rdata"
and find the following error
/bin/bash: mut_annotate: command not found
Error in rule simSummary:
jobid: 17
output: output_bladder/simulated_summary/chasm_sim_summary1.txt
shell:
mut_annotate --log-level=INFO -b data//snvboxGenes.bed -i data//snvboxGenes.fa -c 1.5 -m data/bladder.txt -p 0 -n 1 --summary --seed=$((1*42)) --score-dir=data//scores --unique -r 3 -o output_bladder/simulated_summary/chasm_sim_summary1.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)