checkEnv.py fails when samtools is installed in /usr/bin [conda route]

snandiDS / prokseq-v2.0

MIT License

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checkEnv.py fails when samtools is installed in /usr/bin [conda route] #16

Open osowiecki opened 1 year ago

osowiecki commented 1 year ago

This script is ignoring the configuration file if samtools is present in /usr/bin.

/home/ngs/prokseq/scripts/libmod/checkEnv.py

My system samtools is not compatible with the pipeline. Please make it the default to read the parameter first and then search the system if it fails to find something.