+
Both parent and child tracks within a super-track can have their own description files. If the description file is not present, the corresponding sections of the track settings and details pages are left blank. Only one description page can be associated with composite and multiWig tracks; the file name should correspond to the symbolic name of the top-level track in the composite.
To organize tracks within your track hub, you can utilize the groups setting, which references a separate text file that defines track groups for display under the genome browser graphic.
+
The groups setting can be applied to a UCSC genome, a GenArk assembly, or an assembly hub. These track hub groups are kept separate from other track hubs and the native UCSC Genome Browser track groups, allowing for greater organizational flexibility. For instance, you can add a "genes" group without causing conflicts or confusion.
You can define groups with names like "Category 1", "Category 2", and "Category 3". These group names are specified in the "groups.txt file ", which defines the track groups. Below is an example stanza demonstrating how to define these groups:
name category1
label Category 1name category2
@@ -975,32 +975,31 @@
hubCheck -noTracks http://url.to.hub.txt
The noTracks setting speeds up the validation process but does not check for
the presence or validity of your remotely hosted data track files. This tool checks your hub.txt,
genome.txt, and trackDb.txt settings and displays warnings and errors in bright red font, such
as "Missing required setting..." and
"Cannot open...". The "Display load times" and "Enable
hub refresh" optional settings show the load timing at the bottom of the Genome Browser page
and allow instant hub refresh instead of 5 minute refresh. These options can be checked and
activated by clicking "View Hub on Genome Browser". The following picture shows
the example track grouping hub
with the warning that the hub has no hub description page, no configuration errors,
and "Display load times" checked:
- 
+
The Hub Development tool checks for proper configuration
files and track hub settings, and allows access to debugging settings.
Check hub settings using hubCheck utility
It is a good practice to run the command-line utility hubCheck on your track hub when you
first bring it online and whenever you make significant changes. This utility by default checks
that the files in the hub are correctly formatted, but it can also be configured to check a few
other things including that various trackDb settings are correctly spelled and that they are
supported by the UCSC Genome Browser. You can read more about using hubCheck to check the
compatibility of your hub with other genome browsers below.
Here is the usage statement for the hubCheck utility:
hubCheck - Check a track data hub for integrity.
@@ -1368,68 +1367,68 @@
FAIR data analysis that enables users to streamline and the analysis
of genomic data and serves as a comprehensive toolkit for researchers, scientists, and
bioinformaticians.
The Galaxy platform provides a user-friendly web interface that allows you to host your data. You
can navigate to the Galaxy platform, log in to your account (or
create an account if you haven't already), and use the data upload functionality
provided to host your data. Once uploaded, the data will be stored securely on the platform and made
available for your analysis.
Viewing a Single File Hosted on Galaxy
- To begin, sign into your Galaxy account and then click the "Upload Data" button on
the left-hand side of the page. A pop-up will appear to upload the file to Galaxy.
-
+
- On the pop-up menu, click the "Choose local files" to select the file to host. Once
the file is selected, select the genome and file type from the drop-down menus, and click the
"Start" button. For this example, we will upload a
bigBed file for the
GRCh37/hg19 genome to Galaxy.
-
+
- Once the file is uploaded to Galaxy, it will appear in the "History" section on the
right-hand side. Click on the file to expand the menu, and additional information about the
file such as the file size, format, and the database. Towards the bottom of the menu, five
icons are displayed that perform different functions on Galaxy. Clicking on the
"graph icon" will bring up another menu in the middle of the screen with a link to
visualize the bigBed file on the UCSC Genome Browser.
-
+
Creating and Viewing a Hub Hosted on Galaxy
- Similar to the step in the previous example, sign into your Galaxy account and upload the
files to Galaxy. For this example, we will be uploading a
bigBed, a
VCF, and a
VCF index file
to view on the GRCh37/hg19 genome as a track hub.
-
+
- To create the hub, a URL to each of the files is needed to reference the Galaxy hosted data
inside the hub. Click on each of the three files to expand the menu and display the five icons
at the bottom. Next, click on the "chain-link" icon to copy the URL to the
hosted file. With these three URLs, we can now begin to build the hub.
-
+
- When creating the hub, it is recommended to use the
useOneFile on
setting to have the contents of the genomes.txt, hub.txt, and trackDb.txt files inside of a
single file. With the URLs from the previous step, reference the three files hosted on Galaxy
using the the bigDataUrl and
bigDataIndex trackDb settings. The entire contents of the example hub can
be seen below:
hub myExampleHub
shortLabel Example Hub
longLabel Example Hub Hosted on Galaxy
@@ -1448,101 +1447,101 @@
bigDataIndex https://usegalaxy.org/api/datasets/f9cad7b01a47213595c3df01954cabaf/display?to_ext=binary
track bigBedExample
shortLabel BigBed example
longLabel BigBed example using Galaxy
type bigBed
visibility pack
bigDataUrl https://usegalaxy.org/api/datasets/f9cad7b01a4721358405ebd3fc34f65a/display?to_ext=bigbed
- After creating the hub on your local computer, upload the hub.txt file to Galaxy. Once the
file is on Galaxy, click on the hub.txt file to expand the menu. Again, click on the
"chain-link" icon to obtain the URL to the hub.txt file. Now, navigate to
the UCSC Genome Browser's Track Hubs page
and enter the URL to view the hub.
-
+
-
Alternatively, you can create a URL using the &hubUrl= URL parameter to quickly
share and load the hub with colleagues:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr21:33031468-33034434&hubUrl=https://usegalaxy.org/api/datasets/f9cad7b01a472135a3056c5f93f137db/display?to_ext=txt
Hosting Hubs on CyVerse
CyVerse, previously known as the iPlant Collaborative, is
an NSF-funded site created for assisting data scientists with their data storage and compute
needs. Data hosting by CyVerse is free for academic groups and they support byte-range access,
so they can be used for track hubs. However, Cyverse is sometimes slow,
and may result in error messages if your hub includes many tracks that are
meant to be shown at the same time by your users.
In order to host your data on CyVerse, you first must create an account and then use their
Discovery Environment to upload data.
After creating an account and signing in, access the data screen by clicking the second icon
on the left. Use the "Upload" button on the far right to import data from a URL or
locally from your machine.
- 
+
You can also use the command line utility
iCommands to facilitate bulk transfer of data (best used for
large files in the 2-100 GB range), or use
Cyberduck to bulk transfer up to 80 GB of data in one go.
Once your file is available use the three dots on the far right to click the "Public
Links(s)" option.
- 
+
Select this option for all the files you will be using with the Genome Browser, whether they
are text-based files (trackDb.txt, groups.txt, description.html, etc.) or binary-indexed files
(BAM, bigWig, bigBed, etc.) requiring byte-range access. Note, if you have a dataFile.bam,
you must also have a dataFile.bam.bai file of the matching name and both must have public
links created.
After creating public links to your binary files, you must ensure your text files (i.e., trackDb.txt)
point to the CyVerse locations for the files. For instance, the bigDataUrl setting, will need to point
to the location of the BAM, bigWig, or bigBed (i.e., bigDataUrl https://data.cyverse.org/...
/dataFile.bam).
- 
+
The hub.txt file (if not using the useOneFile on setting) will need to point the related
genomes.txt location, which in turn points to the trackDb.txt location
using these full https://data.cyverse.org/... links as well.
Please see the Using the Discovery Environment wiki page on the CyVerse wiki for more information.
Please direct any questions about CyVerse or the Discovery Environment to their
Contact Us page or "Chat with
Cyverse support" staff directly via the blue question box icon on the top right of the
Discovery Environment page.
- 
+
Note, if you need to replace files once they have been uploaded into CyVerse's DE and Public links
have already been created you will need to force update the CyVerse cache. One way is to go back to the
Public links section and find "Refresh Cache" button. Another way is by hitting Control-Shift-R
in your browser to force reload the file or by sending Cache-Control: no-cache header: curl
--head --header 'Cache-Control: no-cache' https://data.cyverse.org/.../dataFile.bam