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hammerlab / biokepi

Bioinformatics Ketrew Pipelines
Apache License 2.0
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Make MuTect v1 great again #474

Closed armish closed 7 years ago

armish commented 7 years ago

@julia326 found out that mutect v1 has started failing since @smondet's recent migration of biokepi runners from Java 1.7 to 1.8 (c.f. https://github.com/hammerlab/secotrec/issues/64). This is apparently a well-known issue and has been acknowledged by Broad.

This change wraps the mutect tool with a conda environment that comes with openjdk-7.x to make sure it keeps running no matter what the global Java version is.

(Tested and confirmed that this works as intended)

hammer commented 7 years ago

👍🏼 for the fix (makes me think we should bundle a fixed runtime with all log-running tools), 👎🏼 for Trump reference (requires trigger warning)

hammer commented 7 years ago

Gah meant long-running of course