Public Hub QA: Difference between revisions

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==Overview==
== 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.
====Philosophy of QAing Data in a Public Hub====
Based on the data explore whether a data set should overlap or avoid certain regions such as coding exons (or maybe it would be promoters, or areas of open chromatin, or common SNPs, or highly conserved regions, or 5’ UTRs, or  3’ UTRs, or mitochondria, or the sex chromosomes, depending on the type of data, you can ask the hub provider for input to understand expectations of the data if it isn't clear). Using an idea of what the data should be about try to identify at least one native track in the Genome Browser that one might expect to correlate or anti-correlate with the tracks in the hub data set and visually spot check a few.


===Public Hub Overview===
[https://genome.ucsc.edu/cgi-bin/hgHubConnect Public hubs] are track or assembly hubs contributed by the worldwide research community. 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 hubs are made visible by a line the hgcentral*.hubPublic table i.e.:
Public hubs are made visible by a line in the hubPublic table that the QA-er will add to the various hgcentral* databases. For example:


<pre>
<pre>
+--------------------------------------+-----------------------------+------------------------------------------------------------------------------------------------------------------+---------------------+---------+--------+
+----------------------------------------------+-------------------+---------------------------------------+---------------------+---------+--------+--------------------------------+
| hubUrl                               | shortLabel                 | longLabel                                                                                                       | registrationTime    | dbCount | dbList |
| hubUrl                                       | shortLabel       | longLabel                             | registrationTime    | dbCount | dbList | descriptionUrl                |
+--------------------------------------+-----------------------------+------------------------------------------------------------------------------------------------------------------+---------------------+---------+--------+
+----------------------------------------------+-------------------+---------------------------------------+---------------------+---------+--------+--------------------------------+
| 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,  |  
| http://lisanwanglab.org/DASHR/tracks/hub.txt | DASHR small ncRNA | DASHR Human non-coding RNA annotation | 2015-12-20 11:30:47 |      1 | hg19,  | http://lisanwanglab.org/DASHR/ |
+--------------------------------------+-----------------------------+------------------------------------------------------------------------------------------------------------------+---------------------+---------+--------+
+----------------------------------------------+-------------------+---------------------------------------+---------------------+---------+--------+--------------------------------+
</pre>
</pre>


=== UCSC-Hosted Public Hubs ===
== Public Hub QA Process ==  


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 QA process for public hubs is simple: (1) Check that the hub meets our [http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines#Required_Guidelines required guidelines], (2) if so, add it to the public list; if not, work with the contributor to ensure it meets those guidelines. Each section below contains more details as to what steps of the QA process you carry out on each of our sites/machines.  


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.
=== On hgwdev ===


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>).
This is where most of the Public Hub QA process will happen.


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).
==== 1) Add Hub to the hubPublic table on hgwdev ====


==Wrangling Public Hub==
First, run hubPublicCheck on your 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.
<pre>
hubPublicCheck -addHub=http://lisanwanglab.org/DASHR/tracks/hub.txt hubPublic
</pre>


To add the hub to the hubPublic table on dev, follow the below steps about adding the hub to beta, except log onto the dev MySQL server instead of the beta server:
This command will generate the MySQL insert statement needed to add this hub to the hubPublic table. Here is an example command output by hubPublicCheck:
<pre>
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,");
</pre>


hubPublicCheck -addHub=http://johnlab.org/xpad/Hub/UCSC.txt hubPublic
Then, use hgsql to insert the line for this hub into the hubPublic table on dev:
<pre>
hgsql -e “<your hubPublicCheck command here>” hgcentraltest
</pre>


[With commandline utilities that use udcCache, you have to specify the option -udcDir= so that it
==== 2) Display the hub in the Genome Browser and do some minimal QA ====
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 hgcentraltest to change the hubPublic table. The output should look something like:
After adding the new hub to the hubPublic table, connect the hub and view in the Genome Browser. The primary QA you will do is ensuring that the hub meets our [http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines#Required_Guidelines required guidelines], such as checking for track descriptions with contact information.


<pre>
Based on the data, you should explore whether a data set should overlap or avoid certain regions such as coding exons (or maybe it would be promoters, or areas of open chromatin, or common SNPs, or highly conserved regions, or 5’ UTRs, or  3’ UTRs, or mitochondria, or the sex chromosomes, depending on the type of data, you can ask the hub provider for input to understand expectations of the data if it isn't clear). Using an idea of what the data is describing, try to identify at least one native track in the Genome Browser that one might expect to correlate or anti-correlate with the tracks in the hub dataset and visually spot check a few.
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,");
</pre>


Once you have this text, go into hgcentraltest (hgsql hgcentraltest) and paste in the output of hubPublicCheck at the mysql prompt
You should also look for [http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines#Recommended_Guidelines recommended guidelines] that the hub violates. For these recommended guidelines, note those that if fixed would greatly improve the usability of the hub for our users. For example, if a hub contains 300 tracks, but they aren’t organized into composites or superTracks, you should recommend that they group their tracks in a reasonable manner.


You may wish to review engineer feedback providing [http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines Public Hub Guidelines] to refresh areas to examine closely.
===== Notes for Assembly Hubs =====


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  <tt>host <server name></tt> command, e.g. <tt>host genome-euro.ucsc.edu</tt>.
In addition to the normal public track hub QA, there are a few things you should pay attention to:


==Stage the hub on Beta==
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.
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.:


* Check that the 2bit files exist and that the genomes.txt file 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 track description pages)


hubPublicCheck -addHub=http://johnlab.org/xpad/Hub/UCSC.txt hubPublic
* '''Warning:'''  Be sure to check ''all your assemblies on the RR before you release''. We have a lot of unreleased assemblies on hgwdev, a hub developer once developed a hub with preview assemblies, which worked fine on hgwdev, but on the RR such assemblies failed as the data wasn't there.  


[With commandline utilities that use udcCache, you have to specify the option -udcDir= so that it
==== 3) Pass feedback to the hub contributor ====
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:
If during the previous step, you encountered issues with the hub or noticed that it violates some of our required guidelines, pass these on to the hub contributor in an email. When contacting the hub contributor, lay out your feedback in a clear and concise manner, such as through a numbered list. Often it’s helpful to not just point out the issues but to provide a solution as well, especially if it’s the misuse of a trackDb tag.


<pre>
For our “recommended” guidelines, you should only pass on feedback for those items that would greatly increase the usability of the hub. For example, organizing hundreds of loose tracks into a superTrack or composite. When passing along these you should note that the contributor isn’t required to change these things, but that it would greatly increase the usefulness of their hub.  
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,");
</pre>


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).
=== On hgwbeta ===


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.
==== 1) Add the hub to the hubPublic table on hgwbeta ====


==Cursory QA on beta==
Same as the step for adding this hub to hubPublic on hgwdev.
Once the hub is staged on beta do a minimal round of QA - including:


*Making sure the tracks open.
==== 2) Cursory QA on beta ====
*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 [http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines Public Hub Guidelines] to refresh areas to examine closely.


==Push to the RR==
Be sure that the hub and all its tracks load properly on beta. The best way to check this is by clicking the “hide all” button on hgTracks and then navigating to the “Configure” page. On the Configure page, click the “show all” button on the track group for your track hub and then click “submit”. Check that all of the tracks load and that you don’t see any yellow error messages indicating that there were issues loading certain tracks.
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:
=== Release to the RR ===
hgsql -h genome-centdb


Then at the mysql prompt:
Use the same insert statement that you used to add this hub to hubPublic on hgwbeta to add this hub to the hubPublic table on the RR.
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). '''Updating note:''' If you are updating a hub in the future, because perhaps it has changed genomes.txt since you first added it, you may want to run the <code>hubPublicCheck</code> again to get the updated statement and be sure to update at dev,beta, and the RR (we have a [http://genomewiki.cse.ucsc.edu/genecats/index.php/Monitoring_Tasks hubPublicCheck cronjob] that also checks for when remote hubs make changes).
=== Post-RR release ===


Once this is done, update the redmine ticket and notify the hub contributor that their hub is live.
==== 1) Rebuild and push hub search files and tables ====


==Building hub search files/tables==
'''With new Public Hubs (especially with descriptionUrls), once they are on the beta/RR, be sure to build and push an update of the index files'''. <br>
'''With new Public Hubs (especially with descriptionUrls), once they are on the beta/RR, be sure to build and push an update of the index files'''. <br>
1. To build these files navigate to hive and run the doPublicCrawl script.
A. To build these files navigate to hive and run the doPublicCrawl script.
<pre>cd /hive/groups/browser/hubCrawl
<pre>cd /hive/groups/browser/hubCrawl
./doPublicCrawl     
./doPublicCrawl     
</pre>
</pre>
2. The result will be an updated udcCache directory in /hive/groups/browser/hubCrawl/udcCache and an updated hubSearchText table in hgcentraltest. Ask the admins to push these two things to beta:
B. The result will be an updated udcCache directory in /hive/groups/browser/hubCrawl/udcCache and an updated hubSearchText table in hgcentraltest. Ask the admins to push these two things to beta:
<pre>Please push the following directory on hgwdev:
<pre>Please push the following directory on hgwdev:


Line 115: Line 102:
in the hgcentraltest database to hgcentralbeta
in the hgcentraltest database to hgcentralbeta
</pre>
</pre>
3. You should now be able to search parts of the text on the new hub's descriptionUrl, hub's short or long label, assembly, or track labels.  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.
C. You should now be able to search parts of the text on the new hub's descriptionUrl, hub's short or long label, assembly, or track labels.  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.


4. Once you've verified that searching is working on hgwbeta, push the files/table to rr/euro/asia:
D. Once you've verified that searching is working on hgwbeta, push the files/table to rr/euro/asia:
<pre>Please push the following directory on hgwdev:
<pre>Please push the following directory on hgwdev:


Line 137: Line 124:
</pre>
</pre>


==== 2) Notify hub contributor ====
Contact the hub contributor and let them know that they can contact our internal mailing list (genome-www) with any questions or concerns.
==== 3) Send genome-announce email ====
Here are some previous examples of [https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!searchin/genome-announce/public$20hub announcement emails for public hubs.]  It is an opportunity to share a sentence or two about the lab and data (and maybe thank them for creating the public hub). The news could even be tweeted and added to Facebook too.
== QA for UCSC-hosted public hubs ==
Public hubs created by browser engineers are an alternative to native tracks for specialty data. These types of hubs are QAed and released in a very similar manner to externally hosted hubs with a few minor differences.  The main difference is that there is an additional step to push the hub files from the development system to the public download server. UCSC-hosted public hubs were previously hosted on hgwdev in /gbdb/hubs and then pushed to hgdownload for display on the public site. Now we host these hubs on hgwdev in /usr/local/apache/htdocs-hgdownload/hubs/ although they are still pushed to hgdownload for display on the public site. This shift was done to reduce confusion with other /gbdb pushed that normally go to hgnfs1.
You should still review the hub on hgwdev as described above. Since we’re the ones hosting and providing these hubs, it’s alright to be a little more strict in regards to our hub guidelines. Once the hub is looking good on hgwdev, you can release it to the RR using the steps described in the next section.
=== Releasing UCSC-Hosted big data Public Hubs ===


==Releasing UCSC-Hosted big data Public Hubs==
This step is rare and only relevant for a big data hubs that UCSC is hosting.  
This step is rare and only relevant for a big data hubs that UCSC is hosting.  
The main reasoning for implementing the change from /gbdb/hubs is to help ensure there isn't confusion with other /gbdb/ pushes (which the admins normally push to hgnfs1 as those files are often used by internal tracks in the RR). These public hubs don't go that route and instead go to hgdownload.
 
These hubs are made available with a push request from '''/usr/local/apache/htdocs-hgdownload/hubs/''' on hgwdev to '''/mirrordata/hubs''' on hgdownload.  
These hubs are made available with a push request from '''/usr/local/apache/htdocs-hgdownload/hubs/''' on hgwdev to '''/mirrordata/hubs''' on hgdownload.  


Line 159: Line 160:
</pre>
</pre>


It may be useful to note that the UCSC GTEx data has restrictions on access. Apache for hgdownload only allows RR to access the hub data files so the hub displays on the RR only (the hub won't load on other sites, and files can not be directly downloaded -other external Public Hubs have taken similar steps to control their data).
It may be useful to note that the UCSC GTEx data have restrictions on access. Apache for hgdownload only allows RR to access the hub data files so the hub displays on the RR only (the hub won't load on other sites, and files can not be directly downloaded -other external Public Hubs have taken similar steps to control their data).
 
==Send genome-announce email==
 
Here are some previous examples of [https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!searchin/genome-announce/public$20hub announcement emails for public hubs.]  It is an opportunity to share a sentence or two about the lab and data (and maybe thank them for creating the public hub). The news could even be tweeted and added to Facebook too.
 
==Notes for Public Assembly Hub QA==
 
Assembly hubs are new feature released in early 2013. Refer to the [http://genomewiki.ucsc.edu/index.php/Assembly_Hubs 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


* '''Assembly Hub QA Warning:'''  Be sure to check ''all your assemblies on the RR before you release''.  We have a lot of unreleased assemblies on hgwdev, a hub developer once developed a hub with preview assemblies, which worked fine on hgwdev, but on the RR such assemblies failed as the data wasn't there.
== What to do if a Public Hub is down? ==


Then run through the basic public Track Hub QA talked about in the above sections.
If you notice that a hub is consistently down for an extended period of time (3-5 days), then you should contact the hub contributor to let them know that their hub is having issues. We keep a page of the contact information for all of our public hubs here: http://genecats.cse.ucsc.edu/qa/test-results/publicHubContactInfo/publicHubContact.html. We also have a [[Monitoring_Tasks|cronjob]] that checks the status of all of our public hubs, so be sure to check in with the person receiving those emails before sending your message.


[[Category:Browser QA tracks]]
[[Category:Browser QA tracks]]
[[Category:Browser QA]]
[[Category:Browser QA]]

Revision as of 17:22, 6 July 2017

Overview

Public hubs are track or assembly hubs contributed by the worldwide research community. 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 hubs are made visible by a line in the hubPublic table that the QA-er will add to the various hgcentral* databases. For example: 

+----------------------------------------------+-------------------+---------------------------------------+---------------------+---------+--------+--------------------------------+
| hubUrl                                       | shortLabel        | longLabel                             | registrationTime    | dbCount | dbList | descriptionUrl                 |
+----------------------------------------------+-------------------+---------------------------------------+---------------------+---------+--------+--------------------------------+
| http://lisanwanglab.org/DASHR/tracks/hub.txt | DASHR small ncRNA | DASHR Human non-coding RNA annotation | 2015-12-20 11:30:47 |       1 | hg19,  | http://lisanwanglab.org/DASHR/ |
+----------------------------------------------+-------------------+---------------------------------------+---------------------+---------+--------+--------------------------------+

Public Hub QA Process

The QA process for public hubs is simple: (1) Check that the hub meets our required guidelines, (2) if so, add it to the public list; if not, work with the contributor to ensure it meets those guidelines. Each section below contains more details as to what steps of the QA process you carry out on each of our sites/machines.

On hgwdev

This is where most of the Public Hub QA process will happen.

1) Add Hub to the hubPublic table on hgwdev

First, run hubPublicCheck on your hub: 

 hubPublicCheck -addHub=http://lisanwanglab.org/DASHR/tracks/hub.txt hubPublic

This command will generate the MySQL insert statement needed to add this hub to the hubPublic table. Here is an example command output by hubPublicCheck: 

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,");

Then, use hgsql to insert the line for this hub into the hubPublic table on dev: 

hgsql -e “<your hubPublicCheck command here>” hgcentraltest

2) Display the hub in the Genome Browser and do some minimal QA

After adding the new hub to the hubPublic table, connect the hub and view in the Genome Browser. The primary QA you will do is ensuring that the hub meets our required guidelines, such as checking for track descriptions with contact information.

Based on the data, you should explore whether a data set should overlap or avoid certain regions such as coding exons (or maybe it would be promoters, or areas of open chromatin, or common SNPs, or highly conserved regions, or 5’ UTRs, or 3’ UTRs, or mitochondria, or the sex chromosomes, depending on the type of data, you can ask the hub provider for input to understand expectations of the data if it isn't clear). Using an idea of what the data is describing, try to identify at least one native track in the Genome Browser that one might expect to correlate or anti-correlate with the tracks in the hub dataset and visually spot check a few.

You should also look for recommended guidelines that the hub violates. For these recommended guidelines, note those that if fixed would greatly improve the usability of the hub for our users. For example, if a hub contains 300 tracks, but they aren’t organized into composites or superTracks, you should recommend that they group their tracks in a reasonable manner.

Notes for Assembly Hubs

In addition to the normal public track hub QA, there are a few things you should pay attention to:

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 file 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 track description pages)
  • Warning: Be sure to check all your assemblies on the RR before you release. We have a lot of unreleased assemblies on hgwdev, a hub developer once developed a hub with preview assemblies, which worked fine on hgwdev, but on the RR such assemblies failed as the data wasn't there.

3) Pass feedback to the hub contributor

If during the previous step, you encountered issues with the hub or noticed that it violates some of our required guidelines, pass these on to the hub contributor in an email. When contacting the hub contributor, lay out your feedback in a clear and concise manner, such as through a numbered list. Often it’s helpful to not just point out the issues but to provide a solution as well, especially if it’s the misuse of a trackDb tag.

For our “recommended” guidelines, you should only pass on feedback for those items that would greatly increase the usability of the hub. For example, organizing hundreds of loose tracks into a superTrack or composite. When passing along these you should note that the contributor isn’t required to change these things, but that it would greatly increase the usefulness of their hub.

On hgwbeta

1) Add the hub to the hubPublic table on hgwbeta

Same as the step for adding this hub to hubPublic on hgwdev.

2) Cursory QA on beta

Be sure that the hub and all its tracks load properly on beta. The best way to check this is by clicking the “hide all” button on hgTracks and then navigating to the “Configure” page. On the Configure page, click the “show all” button on the track group for your track hub and then click “submit”. Check that all of the tracks load and that you don’t see any yellow error messages indicating that there were issues loading certain tracks.

Release to the RR

Use the same insert statement that you used to add this hub to hubPublic on hgwbeta to add this hub to the hubPublic table on the RR.

Post-RR release

1) Rebuild and push hub search files and tables

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

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

B. The result will be an updated udcCache directory in /hive/groups/browser/hubCrawl/udcCache and an updated hubSearchText table in hgcentraltest. Ask the admins to push these two things to beta: 

Please push the following directory on hgwdev:

/data/apache/userdata/hubCrawl/udcCache/

to the following location on hgnfs1 (Items that are symlinked on dev should become real files on hgnfs1):

/export/userdata/hubCrawl/beta/

Please also push the following table 

hubSearchText

in the hgcentraltest database to hgcentralbeta

C. You should now be able to search parts of the text on the new hub's descriptionUrl, hub's short or long label, assembly, or track labels. 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.

D. Once you've verified that searching is working on hgwbeta, push the files/table to rr/euro/asia: 

Please push the following directory on hgwdev:

/data/apache/userdata/hubCrawl/udcCache/

to the following location on hgnfs1:

/export/userdata/hubCrawl/rr/

and the following location on euro/asia:

/export/userdata/hubCrawl/

Please also push the following table 

hubSearchText

in the hgcentralbeta database to genome-centdb

2) Notify hub contributor

Contact the hub contributor and let them know that they can contact our internal mailing list (genome-www) with any questions or concerns.

3) Send genome-announce email

Here are some previous examples of announcement emails for public hubs. It is an opportunity to share a sentence or two about the lab and data (and maybe thank them for creating the public hub). The news could even be tweeted and added to Facebook too.

QA for UCSC-hosted public hubs

Public hubs created by browser engineers are an alternative to native tracks for specialty data. These types of hubs are QAed and released in a very similar manner to externally hosted hubs with a few minor differences. The main difference is that there is an additional step to push the hub files from the development system to the public download server. UCSC-hosted public hubs were previously hosted on hgwdev in /gbdb/hubs and then pushed to hgdownload for display on the public site. Now we host these hubs on hgwdev in /usr/local/apache/htdocs-hgdownload/hubs/ although they are still pushed to hgdownload for display on the public site. This shift was done to reduce confusion with other /gbdb pushed that normally go to hgnfs1.

You should still review the hub on hgwdev as described above. Since we’re the ones hosting and providing these hubs, it’s alright to be a little more strict in regards to our hub guidelines. Once the hub is looking good on hgwdev, you can release it to the RR using the steps described in the next section.

Releasing UCSC-Hosted big data Public Hubs

This step is rare and only relevant for a big data hubs that UCSC is hosting.

These hubs are made available with a push request from /usr/local/apache/htdocs-hgdownload/hubs/ on hgwdev to /mirrordata/hubs on hgdownload.

Here's an example push request: 

Please push the following file:

/usr/local/apache/htdocs-hgdownload/hubs/newHub/*

from hgwdev --> hgdownload/hgdownload-sd
    (in path, "/usr/local/apache/htdocs-hgdownload/" should become "/mirrordata/" on hgdownload)

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

Reason:  Releasing new UCSC hosted hub newHub to hgdownload.

Thanks!

It may be useful to note that the UCSC GTEx data have restrictions on access. Apache for hgdownload only allows RR to access the hub data files so the hub displays on the RR only (the hub won't load on other sites, and files can not be directly downloaded -other external Public Hubs have taken similar steps to control their data).

What to do if a Public Hub is down?

If you notice that a hub is consistently down for an extended period of time (3-5 days), then you should contact the hub contributor to let them know that their hub is having issues. We keep a page of the contact information for all of our public hubs here: http://genecats.cse.ucsc.edu/qa/test-results/publicHubContactInfo/publicHubContact.html. We also have a cronjob that checks the status of all of our public hubs, so be sure to check in with the person receiving those emails before sending your message.

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