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
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 User Guide. The
-Source
+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
128.114.198.32This will allow connections with the U.S.-based genome.ucsc.edu site, the Europe-based mirror, @@ -182,31 +182,31 @@
STEP 4. You now have all the required files on your local machine and can load this plant assembly hub by using this URL and selecting it under the "group" category where "Plant araTha1" displays:
http://127.0.0.1:1234/cgi-bin/hgGateway?genome=araTha1&hubUrl=http://127.0.0.1:1234/folders/hubExamples/hubAssembly/plantAraTha1/hub.txtSTEP 5. To enable blat you must acquire the gfServer utility. The UCSC Genome Browser and Blat software are free for academic, nonprofit, and personal use. Commercial download and installation of the Blat and In-Silico PCR software may be licensed through Kent Informatics.
You can obtain just the gfServer utility on your GBiB with either of the following commands that 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.gi.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
isPcr yourLab.yourInstitution.edu 17779