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broadinstitute / gdctools

Python and UNIX CLI utilities to simplify interaction with the NIH/NCI Genomics Data Commons
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major bug: reference files not installed #70

Closed noblem closed 6 years ago

noblem commented 6 years ago

The report code looks for reference files, e.g. sampleType.txt, when generate sample summary reports. It appears that we've created this 

/xchip/gdac_data/gdc/reference

manually for our production system, because when I try to generate reports locally on my laptop (which doesn't have a ./reference directory anywhere) the report code aborts.

These files exist in the ./tests/reference directory of the repo, and should be installed. They also need to be generalized to be usable beyond TCGA programs, but since other programs have adopted TCGA metadata standards this may not be a showstopper yet.

noblem commented 6 years ago

This was addressed in v0.2.7 (commit https://github.com/broadinstitute/gdctools/commit/85f0c41762c51e96f8898b2bafacf27f0163e018)