Public Hub QA

Overview

Public hubs are made visible by a line the hgcentral*.hubPublic table i.e.:

+--------------------------------------+-----------------------------+------------------------------------------------------------------------------------------------------------------+---------------------+---------+--------+
| hubUrl                               | shortLabel                  | longLabel                                                                                                        | registrationTime    | dbCount | dbList |
+--------------------------------------+-----------------------------+------------------------------------------------------------------------------------------------------------------+---------------------+---------+--------+
| http://johnlab.org/xpad/Hub/UCSC.txt | DRS PolyA site & Expression | Genomewide expression & Polyadenylation landscape of cancer using Direct RNA sequencing (Tissues and Cell lines) | 2012-05-15 09:50:09 |       1 | hg19,  | 
+--------------------------------------+-----------------------------+------------------------------------------------------------------------------------------------------------------+---------------------+---------+--------+

The entry in the hubPublic table on hgwdev (i.e. in hgcentraltest) will be added by the developer and the developer will work with the authors to get it into basic acceptable shape (much like they would do for a regular data track) before handing it off to QA.

Stage the hub on Beta

Begin by running hubPublicCheck to generate the insert statement needed to add the line to hgcentralbeta.hubPublic. You will need to get the hub url either from the redmine ticket or from the instance of it on hgwdev i.e.:

hubPublicCheck -addHub=http://johnlab.org/xpad/Hub/UCSC.txt hubPublic

This outputs the insert statements you will need to insert into hgcentralbeta to change the hubPublic table. The output should look something like:

mysql> insert into hubPublic (hubUrl,shortLabel,longLabel,registrationTime,dbCount,dbList) values ("http://zlab.umassmed.edu/zlab/publications/UMassMedZHub/hub.txt","UMassMed ZHub", "UMassMed H3K4me3 ChIP-seq data for Autistic brains",now(),1, "hg19,");

Once you have this text, go into hgcentralbeta (hgsql hgcentralbeta) and paste in the output of hubPublicCheck at the mysql prompt. This should cause the hub you are testing to appear on beta immediately (i.e. you don't need to do a make). (Before adding you can use the commands "mysql> select * from hubPublic \G" to show all and again afterward to confirm addition).

Cursory QA on beta

Once the hub is staged on beta do a minimal round of QA - including:

• Making sure the tracks open.
• Make sure there aren't too many tracks on by default - the hub should load quickly, if not you might need to ask the contributor to reduce the number of tracks on by default
• Checking that tracks have description pages.
• Making sure that the authors' email address is prominently listed in the description pages (so our users can contact them with questions).

Push to the RR

Once you've verified the hub is functioning and looks reasonable you can "push" it to the RR by performing the analogous insert into the hubPublic table on the RR (i.e. in hgcentral).

To go into hgcentral on hgwdev type at the prompt: hgsql -h genome-centdb

Then at the mysql prompt: use hgcentral

Paste in the same insert statement you input on beta (you don't need to rerun hubPublicCheck again on the RR - just paste the same text in).

Once this is done update the redmine ticket and notify the developer that the hub is on the RR so that he/she can tell the contributor that their hub is live.