GRC Patch Release

The GRC Patch Release track is different from other tracks in that you are technically also releasing the patch assembly to the RR. The release of the patch assembly is what allows the links in the hgc page to display the DNA from the patched assembly. Note that in the automatic creation of an assembly, there are many tables and files created that are not necessary for this track. There are only select things that need to be created and pushed in order to allow the GRC Patch Release track to function.

These are the extra steps you take to achieve this (for hg19), in addition to the normal steps of pushing the tables and associated files.

Stage the track on beta

1. Make patch database on beta:

hgwbeta> hgsql
hgwbeta> create database hg19Patch#;

2. Push the chromInfo table to mysql beta

hgwdev> sudo mypush hg19Patch# chromInfo mysqlbeta

3. Add the necessary lines to hgcentralbeta.dbDb

hgwdev> hgsql -Ne 'select * from dbDb where name like "hg19Patch#"'  hgcentraltest > dbDbHg19Patch

Then edit dbDbHg19Patch2 and change the active column to be 0 rather than 1. This will prevent the database from showing in on hgGateway.

hgwbeta> hgsql -e "load data local infile 'dbDbHg19Patch' into table dbDb" hgcentralbeta

4. Add the necessary lines to hgcentralbeta.genomeClade

hgwdev> hgsql -Ne 'select * from genomeClade where genome like "GRCh37.p#"' hgcentraltest > genomeCladeHg19Patch
hgwbeta> hgsql -e "load data local infile 'genomeCladeHg19Patch' into table genomeClade" hgcentralbeta

5. Ask for push of /gbdb/hg19Patch#/hg19Patch#.2bit and /gbdb/hg19/hg19Patch#/* (which should contain the assembly in .fa file format) from hgwdev to hgnfs1.

Push the track to the RR

IMPORTANT!! do this before pushing any of the other tables or files

1. Ask the admins to rsync the hg19Patch# database to the RR from mysqlbeta.

2. Add the necessary lines to hgcentral.dbDb, using the same file that you used to load the lines into hgcentralbeta.dbDb

hgwdev> hgsql -h genome-centdb -e "load data local infile 'dbDbHg19Patch' into table dbDb" hgcentral

3. Add the necessary lines to hgcentral.genomeClade, using the same file that you used to load the lines into hgcentralbeta.genomeClade

hgwdev> hgsql -h genome-centdb -e "load data local infile 'genomeCladeHg19Patch' into table genomeClade" hgcentral