Public Hub QA

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Revision as of 21:06, 29 August 2016 by Brianlee (talk | contribs) (→‎Notes for Public Assembly Hub QA: adding defaultPos, scientificName, organism, description recommendation)
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Overview

Process Overview

Public hubs are wrangled and QA'd by the UCSC GB QA team. The QAer should work directly with the data submitter from the start to get the track hub in the correct format, etc. Then the QA person QA's the hub (a light QA compared with native tracks) and releases it. QA communicates directly with the data contributor throughout the process. If QAer needs technical help, please contact the Project Manager or an engineer.

Public Hub 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,  | 
+--------------------------------------+-----------------------------+------------------------------------------------------------------------------------------------------------------+---------------------+---------+--------+

UCSC-Hosted Public Hubs

Public hubs created by browser engineers are an alternative to native tracks for specialty data. This kind of hub is QAed and released slightly differently from externally hosted hubs. The main difference is that there is an additional step to push the hub files from the development system to the public download server.

The first step is to review the hub, as described below, with the files hosted on genome-test so the developer can easily change them during QA. You can do this from the browser on genome.ucsc.edu, adding the hub URL on genome-test (e.g. http://genome-test.cse.ucsc.edu/gbdb/hubs/<your-hub>/hub.test.txt) via the 'My Hubs' panel of the Track Data Hubs page.

After you have completed review and the developer has made any changes needed, you will request a push of the hub files listed by the developer (e.g. in the file /hive/data/gbdb/hubs/<your-hub>/filelist.txt) to the download server (directory /mirrordata/hubs/<your-hub>).

After sanity checking the hub on hgdownload (e.g at http://hgdownload.soe.ucsc.edu/hubs/<your-hub>/hub.txt), you can proceed with the instructions below for adding to the hubPublic table. (NOTE: The additional testing on hgwbeta mentioned below is probably unnecessary).

Wrangling Public Hub

The entry in the hubPublic table on hgwdev (i.e. in hgcentraltest) will be added by the QAer and that QAer will work with the authors to get it into basic acceptable shape before QAing it. If the QAer has technical questions about wrangling the track, s/he should ask the Project Manager or an engineer for advice/assistance.

You may wish to review engineer feedback providing Public Hub Guidelines to refresh areas to examine closely.

Note, if the hub submitter is looking to limit IP address access to only the Genome Browser public site, don't forget to include genome-euro. You can find the IP address for a server by using the host <server name> command, e.g. host genome-euro.ucsc.edu.

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

[With commandline utilities that use udcCache, you have to specify the option -udcDir= so that it uses some place other than the nearly useless default value /tmp/udcCache, since some other user almost always beats you to it and you can't write there anymore. So, when running hubCheck, specify either "-udcDir=." or "-udcDir=$HOME" or "-udcDir=$HOME/udcCache"]

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 -h mysqlbeta 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).

Note, make sure that the order of the assemblies in the dbList field matches the order of assemblies in the hub's genomes.txt file. The first assembly in the dbList field determines the default assembly that will show up when connecting the assembly hub.

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.
  • Review the shortLabels to see if any need to be shortened by displaying all tracks in dense. The shortLabel text should be under 17 characters, or meaningful information may be cut off from display.
  • The length for a longLabel should be about 75 characters.
  • Making sure that the authors' email address is prominently listed in the description pages (so our users can contact them with questions).
  • Take a moment to review the Public Hub Guidelines to refresh areas to examine closely.

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 hub contributor that their hub is live.

With new Public Hubs (especially with descriptionUrls), once they are on the RR, be sure to build and push an update of the index files.
1. To build these files navigate to hive and run the doPublicCrawl script. 

 
cd /hive/groups/browser/hubCrawl
./doPublicCrawl

2. The result will be updated public.ix and .ixx files on gbdb,request these get pushed out: 

Please push the following files:

/gbdb/hubs/public.ix
/gbdb/hubs/public.ixx

from hgwdev --> hgnfs1

3. You should now be able to search parts of the text on the new hub's descriptionUrl or even the hub's short or long label and assembly. For example a search of methpipe matches a line on the DNA Methylation descriptionUrl: http://smithlabresearch.org/software/methbase/ or hg38 pulls up all the hg38 hubs.

Notes for Public Assembly Hub QA

Assembly hubs are new feature released in early 2013. Refer to the Assembly Hubs page on the public wiki for more info on how to create your own.

The QA for a public Assembly Hub is very similar to that of a public Track Hub, although there are a few things unique to an Assembly Hub.

  • Check that the 2bit files exist and that the genomes.txt files points to the correct 2bit
  • Make sure the correct labels show up in drop down menus on the gateway page
  • Make sure contact information is clearly displayed on all description pages (gateway description, and the track description pages)
  • Strongly suggest the hub add these settings in each genome's entry in genomes.txt (You can explain to them that the last 3 settings will make it easier to find each assembly's hub species in hgGateway by UI search) :
    • defaultPos, scientificName, organism, description


Then run through the basic public Track Hub QA talked about in the above sections.

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