Difference between revisions of "Command line options"
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| + | <strong>Installation</strong> | ||
| + | To use GenomeView on your local PC, you first have to <a href="http://downloads.sourceforge.net/genomeview/">download a local copy</a>. | ||
| + | |||
| + | Extract the contents of the zip file to a directory where you want to install GenomeView. | ||
| + | |||
| + | Add this directory to the 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. | ||
| + | |||
| + | <strong>Use locally</strong> | ||
| + | You can start GenomeView by issuing the following command at the prompt | ||
| + | <code>java -Xmx900m -jar genomeview-<version>.jar</code> | ||
| + | where <version> corresponds to the version number of the package you downloaded. At the time of writing this was 669 so you would type: | ||
| + | <code>java -Xmx900m -jar genomeview-669.jar</code> | ||
| + | |||
| + | <strong>Loading files on start-up</strong> | ||
| + | You can instruct GenomeView to load files when it starts. All file names and URLs that are specified will be loaded. There are a few options you can use. Files are loaded concurrently, unless the --file or --url switch is used. | ||
| + | |||
| + | See the <a href="/content/command-line-options">command line options page</a> for more details. | ||
| + | |||
| + | Some examples: | ||
| + | <code> | ||
| + | $>java -Xmx900m -jar genomeview-669.jar --file seq.fasta | ||
| + | </code> | ||
| + | This command will start GenomeView with seq.fasta loaded. | ||
| + | |||
| + | <code> | ||
| + | $>java -Xmx900m -jar genomeview-669.jar --position 2000:3500 --file seq.fasta feat.embl pred.embl add.embl | ||
| + | </code> | ||
| + | Will start GenomeView with all the specified files loaded, but seq.fasta will be loaded first and zoomed to the region 2000-3500. | ||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
== Available options == | == Available options == | ||
Options for use on the command line or with website integration. | Options for use on the command line or with website integration. | ||
Revision as of 20:40, 18 November 2013
Installation To use GenomeView on your local PC, you first have to <a href="http://downloads.sourceforge.net/genomeview/">download a local copy</a>.
Extract the contents of the zip file to a directory where you want to install GenomeView.
Add this directory to the 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.
Use locally
You can start GenomeView by issuing the following command at the prompt
java -Xmx900m -jar genomeview-<version>.jar
where <version> corresponds to the version number of the package you downloaded. At the time of writing this was 669 so you would type:
java -Xmx900m -jar genomeview-669.jar
Loading files on start-up You can instruct GenomeView to load files when it starts. All file names and URLs that are specified will be loaded. There are a few options you can use. Files are loaded concurrently, unless the --file or --url switch is used.
See the <a href="/content/command-line-options">command line options page</a> for more details.
Some examples:
$>java -Xmx900m -jar genomeview-669.jar --file seq.fasta
This command will start GenomeView with seq.fasta loaded.
$>java -Xmx900m -jar genomeview-669.jar --position 2000:3500 --file seq.fasta feat.embl pred.embl add.embl
Will start GenomeView with all the specified files loaded, but seq.fasta will be loaded first and zoomed to the region 2000-3500.
Available options
Options for use on the command line or with website integration.
| --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 <url or file > | 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 <a href="/content/configuration">configuration</a> 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 |