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We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Update: July 26, 2019
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
MySQL cache migration when updating Cromwell version
awacs
Member ✭
Answers
Database migration are generally automatic when updating Cromwell. Sometimes, there are requirements that need to be completed (i.e, config changes) for a migration to run successfully and these are usually documented in the Cromwell release notes. For example, there is a mysql flag that needs to be set as a part of updating to latest release, Cromwell v27, and there is detailed documentation on how to set that flag.
The IT services at my workplace does not allow me to set GLOBAL mysql flags. Is there a way to do it in session?
Yes you should be able to set this value using
SET GLOBAL group_concat_max_len=XXXX.I meant I can't do that because I don't have SUPER permissions, so I can't do SET GLOBAL.
whoops I meant
SET SESSION