Requests for liftOver files

Overview

The MLM FAQ on LiftOver files shares some guidelines:

liftOver files for assemblies with no browser

We do not provide liftOver files for assemblies for which we do not have at least a minimal browser. If a user requests such a file, please point them to this wiki page and wish them luck!

liftOver file requests for assemblies with a browser

When a specific liftOver file is requested from a user for an existing browser, we should definitely consider making it. It should go through the usual process (make a redmine, assign to an engineer, place in pushQ, QA and release). QA can do a minimal QA job on it (does it work? does it show up?) before pushing it to hgdownload and enabling it on the RR. There is no need to create companion net/chain tracks (unless the user specifically asked for that). The MLM who received the question is not responsible for QAing the liftOver file (it should just go into the pushQ like all data). After it is released, whoever QAd it should contact the user to let them know that it's available.

Here is a quick review of the process

push the files in /gbdb/ on hgwdev to hgnfs1

These files have the same name and live in the same place as hgdownload-test, but are what is used by the CGIs to allow lifting.

edit hgcentral on beta and the RR once gbdb goes through

The lines on dev in hgcentraltest that allow the /gbdb/ files to load in the CGIs need to added to hgcentralbeta and hgcentral.

push the files from hgdownload-test to hgdownload

To make the files available for download, a push of the files to hgdownload is also needed.

push the files in /gbdb/ on hgwdev to hgnfs1

Here is an example push email where mm10 <---> danRer10 liftOver files and rn6 <---> danRer10 liftOver files and hg19 <---> danRer10 files are being released.

Hi Pushers,

Please push:

/gbdb/mm10/liftOver/mm10ToDanRer10.over.chain.gz
/gbdb/danRer10/liftOver/danRer10ToMm10.over.chain.gz
/gbdb/rn6/liftOver/rn6ToDanRer10.over.chain.gz
/gbdb/danRer10/liftOver/danRer10ToRn6.over.chain.gz
/gbdb/hg19/liftOver/hg19ToDanRer10.over.chain.gz
/gbdb/danRer10/liftOver/danRer10ToHg19.over.chain.gz

      from hgwdev --> hgnfs1/genome-euro/-asia

Note that items that are symlinked on hgwdev should become real files on hgnfs1.

Reason: Releasing LiftOvers as part of MLQ ######

Thanks,

This push will make the files available on both hgwbeta and the RR as hgnfs1 is shared by both of them.