After you installed GenomeView, you have the executable jar file on your machine. Add this jar file to the java CLASSPATH if you want GenomeView to be accessible from anywhere on your system. Alternatively you can always start from this directory or you can qualify the full path to the jar-file each time you start GenomeView.
You can start GenomeView from the commandline by issuing the following command at the prompt
java -jar genomeview.jar
Options for use on the command line or with website integration.
| option | explanation |
|---|---|
--file <file> |
Load this file first, all other files will be loaded concurrently after this files has finished |
--url <url> |
Load the data from this url first. After this has finished, all other files will be loaded concurrently |
--session <file or url> |
Load the session from this URL or file. This parameter will override all others. |
--config <file or url> |
Load extra configuration options from this file or URL. This configuration will override default and user configuration. See Configuration for more details. |
--position <position> |
Zoom to the supplied position on start-up. You need to use this in conjunction with the --url or --file option. First that file or url will be loaded and then GenomeView will zoom to the supplied position. The position is in the format <entry>:<start position>:<end position> The entry part can be omitted in which case it becomes <start position>:<end position> |
| remaining arguments | Load all remaining files and URLs specified on the command line |
Additionally, there are the standard java options like -Xmx to get extra memory.
- Start up with 10GB memory
java -Xmx10g -jar genomeview.jar
- Load seq.fasta on startup (use --url for a url)
java -jar genomeview.jar --file seq.fasta
- start GenomeView with 10g of main memory available and all the specified files loaded, but seq.fasta will be loaded first and zoomed to the region 2000-3500
java -Xmx10g -jar genomeview.jar --position 2000:3500 --file seq.fasta feat.embl pred.embl add.embl