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 for an Assembly Hub for details.
+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. See the -section Starting a Blat enabled Assembly Hub on GBiB for more +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.
From the location of yourAssembly.2bit file,
http://yourURL/yourAssembly/yourAssembly.2bit, you can start two gfServers, specifying
a port for the assembly hub to access amino acid sequence, 17777 -trans, or DNA
sequence, 17779, in this example:
gfServer start localhost 17777 -trans -mask yourAssembly.2bit &
gfServer start localhost 17779 -stepSize=5 yourAssembly.2bit &-Then you can edit the genomes.txt file of your assembly hub to include two lines in the stanza +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.
A dynamic BLAT server is specified with the
dynamic argument to
the blat or transBlat specification, followed by
the gfServer dynamic root-relative path of the directory
containing the 2bit and gfidx files, named in the form
myGenome.2bit - two-bit format genomic sequence
myGenome.untrans.gfidx - untranslated index, built by gfServer index
@@ -191,31 +192,31 @@
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
128.114.198.32This will allow connections with the U.S.-based genome.ucsc.edu site, the Europe-based mirror, the Asia-based mirror, and the UCSC development server.
-STEP 1. Acquire and install Genome Browser in a Box: http://genome.ucsc.edu/goldenPath/help/gbib.html. You may also wish to read this UCSC blog post.
STEP 2. With your GBiB operational, use your computer's terminal program to ssh
into your GBiB:
ssh browser@localhost -p 1235, using browser for the password.
STEP 3. Navigate to the GBiB's /folders directory and use sudo to wget this assembly
hub:
cd /folders
sudo wget -r --no-parent --reject "index.html*" -nH --cut-dirs=3 http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/@@ -234,31 +235,32 @@ will create a bin directory and install the tool. The commands use the North American and the European download servers respectively.
mkdir ~/bin -p; rsync -avP hgdownload.soe.ucsc.edu::genome/admin/exe/linux.x86_64/blat/gfServer ~/bin/mkdir ~/bin -p; rsync -avP hgdownload-euro.soe.ucsc.edu::genome/admin/exe/linux.x86_64/blat/gfServer ~/bin/
The GBiB also includes a tool you can run on the command line to download an entire suite of tools
including gfServer: gbibAddTools
STEP 6. Navigate to the genomes.txt file of this assembly hub:
cd /folders/hubExamples/hubAssembly/plantAraTha1/
Edit the currently commented-out blat lines with sudo vi genomes.txt and
use "x" when the cursor is over the # at the start of the line to remove it
and :w! to save the changes and :q to quit.
blat localhost 17779
-transBlat localhost 17777
Please note that if you loaded your hub earlier, it will take five minutes (300 seconds)
for the browser to check for any changes to genomes.txt, and that this delay can be
shortened temporarily by adding &udcTimeout=10 to the URL. See more information in the
Debugging and Updating section of the
Track Hub User Guide.
STEP 7. Change directories to the 2bit file:
cd /folders/hubExamples/hubAssembly/plantAraTha1/araTha1Run the two gfServer commands to start the blat servers:
gfServer start localhost 17777 -trans -mask araTha1.2bit &
gfServer start localhost 17779 -stepSize=5 araTha1.2bit & STEP 8. Load this plant assembly hub by using this URL and selecting it under the