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arq5x / gemini

a lightweight db framework for exploring genetic variation.
http://gemini.readthedocs.org
MIT License
317 stars 119 forks source link

PostgreSQL, what driver/gemini version(s) are compatible? #923

Open JHibbard opened 5 years ago

JHibbard commented 5 years ago

Hello, I loaded a gemini database into PostgreSQL with vcf2db, but cannot find a compatible driver/gemini combination. I get various errors based on the combination used, most centered on how strings are handled (text_factory) or on decompressing fields. I've tried psycopg2, pg8000, and pygresql drivers with gemini v0.20.1 and v0.30.2. Is there a recommended setup for PostgreSQL databases? If not, what non-sqlite database systems are likely to work with the new vcfanno/vcf2db workflow? If it helps, I can provide a docker images and a compose file with my exact setup. Thanks again for all your help!

brentp commented 5 years ago

I think probably the code for non-sqlite DBs has bitrot and does not support other databases. I will accept PR's to fix this, but I can not maintain across DBs.