cd /folders
sudo wget -r --no-parent --reject "index.html*" -nH --cut-dirs=3 http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/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.
+You can obtain just the gfServer utility on your GBiB with the following command that +will create a bin directory and install the tool: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 Please note that if you loaded your hub earlier, it will take five minutes (300 seconds)