UCSF-Costello-Lab / LG3_Pipeline

The original LG3 pipeline

https://github.com/UCSF-Costello-Lab/LG3_Pipeline

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Make it possible to override the default software paths #157

Closed HenrikBengtsson closed 2 years ago

HenrikBengtsson commented 2 years ago

Related to #151. It is currently (tried with version 2021-05-26) not possible to override the default software version, without editing the source code.

Suggestion

Make it possible to override these internal settings using environment variables, e.g.

export MUTECT=/home/shared/cbc/software_cbc/mutect-1.1.1/muTect-1.1.1.jar

Ideally this could be also done in something like a ./.lg3.conf file.

HenrikBengtsson commented 2 years ago

Added to branch next-release, which is clean fork off the 2021-05-26 release.