STEP 1: In a publicly-accessible directory, copy the hub.txt, genomes.txt, trackDb.txt files using the following command:
wget -r --no-parent --reject "index.html*" -nH --cut-dirs=3 http://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/
Alternatively, if you do not have wget installed, use curl:
curl -O http://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt
curl -O http://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/genomes.txt
mkdir hg19
cd hg19
curl -O http://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hg19/trackDb.txtIf you do not have curl, you can alternatively use a text editor and directly recreate the above three files.
+Note: there is now a useOneFile on hub setting that allows the hub
+properties to be specified in a single file. More information about this setting can be found on the
+Genome Browser User Guide.
STEP 2: Paste your hub.txt link (http://yourURL/hub.txt) into the
My Hubs tab of the Track Data Hubs page,
then click the "Use Selected Hubs" button. It should work the same as pasting the original
hub.txt file:
http://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txtSTEP 3: Congratulations! Your hub should display! If you are not already browsing the hg19 assembly on chr21, change assemblies and navigate to the gene SOD1 to see data displayed for each of the hub's BAM, bigWig, bigBed, and VCF tracks.
If you are having problems, be sure all your files and the hg19 directory are publicly-accessible. For hubs to work, your server must also accept byte-ranges. You can check using the following command to verify "Accept-Ranges: bytes" displays: