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PharmGKB / PharmCAT

The Pharmacogenomic Clinical Annotation Tool
Mozilla Public License 2.0
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Is it possible to use exemptions.json without building from source? #153

Closed hudja closed 1 year ago

hudja commented 1 year ago

Hello,

I use the latest 2.7.1 version and I cannot find the way to specify exemptions.json. Do I need to build from source for that? I tried, but my ./gradlew test fails. I found an old issue where json was specified with -na flag, but I cannot find this flag anymore.

Thank you!

markwoon commented 1 year ago

You should not need to specify exemptions.json.

Can yo uplease provide more details on what you're trying to do? Are you just checking out the source from GitHub and running ./gradlew test? If so, please add the console log to to the issue.

hudja commented 1 year ago

I would like to exclude a couple of star alleles from the detection list, but I think I figured it out. I just use -def flag and point to the following folder PharmCAT-2.7.1/src/main/resources/org/pharmgkb/pharmcat/definition/alleles/. I edited exemptions.json inside this folder and it seems working.