Fathmm mysql dump into Postgres

Operations
1

Hi all,

For the FATHMM step of the release/ETL pipeline, the documentation FATHMM.md in dcc-release states to load a dump file downloaded from http://fathmm.biocompute.org.uk/database/fathmm.v2.3.SQL.gz into a running postgres instance.

Only, this file is a mysql dump file, and does not load into postgres. Is this documentation out of date? Do you have a process that accomplishes this well? Or do you think the best solution is to load into mysql, dump out as a tsv and then load into postgres?

Thanks,
Georgia

2

Hi,

We have now made this available here:

https://artifacts.oicr.on.ca/artifactory/dcc-binaries/fathmm-db/2.3/fathmm.v2.3.postgres.tar.gz

see https://github.com/icgc-dcc/dcc-release/blob/develop/FATHMM.md for details

3

Thanks so much! That’s perfect.