Configuring a Genome Server

Upload a new genome to your own server to share with others:

1. Use the steps described in Loading a Genome to create an initial .genome file and sequence directory.  The sequence directory contains a file for each chromosome/contig sequence in the genome. 
2. Copy the sequence directory to a web-accessible directory.
3. Copy the .genome file (which is a zip archive) to a temporary directory and unzip it.
4. Remove the .genome file from the temporary directory.
5. Open the property.txt file in a text editor and edit the following properties:
   • id: Unique identifier for the genome (for example, "hg18"). This property is input to some commands in igvtools. 
   • name: This is the name that appears in the pull-down genome list in IGV.
   • sequenceLocation: http:// <path to sequence directory> (this is the location of the sequence directory discussed in step 1 & 2)
6. Zip all the files in the temporary directory, including the edited property.txt file, and name the resulting archive <id>.genome.  This naming convention is mandatory for igvtools.
7. Copy the <id>.genome file to a web-accessible directory.
8. To make your genome appear in the users' pull-down list, create a genomes list file. The IGV default genomes list file can be used as a starting point. Each line in the genomes list is formatted as follows:
   

   Format	<name>  *tab*  <URL of the .genome file>  *tab*  <id>
   Example	Human hg18         http://www.broadinstitute.org/igvdata/genomes/hg18.genome         hg18

9. To test in IGV, change the genome URL in the Advanced preferences tab (View>Preferences) to: http://<path to your genomes.txt file>.  You must quit IGV and restart for this preference to take effect. The genome should appear in the drop-down list.