Configuring a Genome Server

To upload a new genome to your own server so you can share it with others:

1. Use the steps here  ("Importing a Genome") to create an initial .genome file and sequence directory.   The product of this step will be a ".genome" file and a 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. The following properties need to be edited: 

   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 users' pull-down genome list in IGV.
   sequenceLocation: http:// <path to sequence directory> (this is the location of the sequence directory discussed in step #1)

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, you will need to 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:

        <name> <tab> <URL of the .genome file> <tab> <id>

   for 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.