Assembly Hubs allow researchers to create Track Data Hubs on assemblies that are not in the UCSC Browser. By including the underlying reference sequence in UCSC twoBit format, as well as data tracks, researchers can browse and annotate any genome. We may have a GenArk Hub of your genome, or you can visit our assembly request page and we can build an assembly hub for you.
For more information please refer to the -Assembly Hub Wiki. +Assembly Hub User Guide. Below is also a section about starting GBiB Assembly Hubs.
STEP 1: In a publicly accessible directory, copy this Arabidopsis thaliana plant assembly hub, which includes an araTha1.2bit file, using the following wget command:
wget -r --no-parent --reject "index.html*" -nH --cut-dirs=3 http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/Alternatively, if you do not have wget installed, you can curl these files individually. Perform the curl -O option in the location you wish to copy the files:
curl -O http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txtIf you use curl, be sure to recreate the structure with matching araTha1 and araTha1/bbi directories. Double check you have all the files by looking here:
http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/ @@ -46,64 +46,63 @@
This URL should work the same as using the original data just copied:
http://genome.ucsc.edu/cgi-bin/hgHubConnect?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt STEP 3: Congratulations! Your assembly hub should display!
If you are having problems, be sure all your files and the directories are publicly accessible. You may also wish to reset the browser occasionally to clear all existing data. For hubs to work, your server must also accept byte-ranges. You can check using the following command to verify "Accept-Ranges: bytes" displays:
curl -I http://yourURL/hub.txtNow that you have the assembly hub copied from above, you can copy the directory and start to edit some of the documents such as genomes.txt, groups.txt, and trackDb.txt to understand how they work. -Refer to the Assembly -Hub Wiki to understand how to build a twoBit file for +Refer to the Assembly Hub User Guide to +understand how to build a twoBit file for your own original fasta files. Read more about trackDb settings in the definition document.
This assembly hub is a an abbreviated version of a larger plant assembly Public Hub. You can explore the larger hub structure here.
Please note that the Browser waits 5 minutes before checking for any changes to these files.
When editing hub.txt, genomes.txt, trackDb.txt, and related hub files, shorten this delay by
adding udcTimeout=1 to your URL. For more information, please see the
Debugging and Updating Track Hubs section of
the Track Hub User Guide. Also, for more detailed
instructions on setting up a regular hub, please see the Setting Up Your Own Track Hub section of the Track Hub User Guide.
By running gfServers from your institution, you can enable blat on your assembly hubs. See Starting Blat and In-Silico PCR for an Assembly Hub for details.
With an operational installation of Genome Browser in a Box (GBiB), you can quickly and easily acquire an example assembly hub and run gfServers locally on the GBiB to enable Blat and In-Silico PCR. See the section Starting a Blat and In-Silico PCR enabled Assembly Hub on GBiB for more information.
Then you can edit the genomes.txt file of your assembly hub to include three lines in the stanza referring to yourAssembly, that would have matching port numbers:
transBlat yourLab.yourInstitution.edu 17777
blat yourLab.yourInstitution.edu 17779
isPcr yourLab.yourInstitution.edu 17779
The assembly hub can be configured to talk to a dynamic BLAT server that loads
a pre-built index when started by an xinetd super-server. This
allows genomes to have a blat server without needing it to be resident in
memory at all times. See
Running your own gfServer
and
-Adding BLAT servers
+Adding BLAT servers
for details on how to setup dynamic BLAT servers
See an example genomes.txt with commented out lines
here, and please note the uppercase "B" in transBlat. For more
information, see the "Adding BLAT servers" section of the
-Assembly Hub Wiki. The
+Assembly Hub User Guide. The
Source
Downloads page offers access to utilities with pre-compiled binaries such as gfServer found in
a blat/ directory for your machine type here and further blat documentation
here. Please note that because the -mask option in the above 17777
-trans gfServer option will mask all lower-case sequence from being matched, you may not
wish to include it. See the above blat links and gfServer usage statement for more information.
If you have trouble connecting your blat servers with the browser or if the browser cannot access your files, check if your institution has a firewall that prevents the browser from sending multiple inquiries. If this is the case, ask your systems administrator to add the following IP addresses as exceptions so that access is not limited.
128.114.119.*
129.70.40.99
134.160.84.67