We recommend that you run Caryoscope directly from the supplied link on the website, since this ensures that you will always be using the latest version of the application.
To run Caryoscope directly from the Web, go to the Getting Caryoscope page on the Caryoscope website and click on the Run Caryoscope now! link. If your system is already configured correctly, Caryoscope should start running without any need for active installation of any software.
If clicking on the link does not start Caryoscope, it is likely that you do not have Java Web Start installed on your system. In this case, please download and install Java Web Start and try again.
If you wish to install Caryoscope locally, you should download it as a ZIP file from the website. Upon expanding the ZIP file of version x.y.z of the application, you should see the following folder structure:
The doc folder contains copies of the document you are now reading as a set of HTML pages and in Portable Document Format. The file caryoscope-run.jar contains the application code.
To run your local installation of Caryoscope, the easiest way is to navigate to the caryoscope-run.jar file using your system's graphical interface (e.g., the Explorer or Finder). Double-click directly on the file to run Caryoscope.
If Caryoscope does not start this way, you may not have the Java Runtime Environment installed on your system. In this case, please download and install the Java Runtime Environment and try again.
Running Caryoscope from the command line is useful in two cases:
- To preload some information or settings into the Caryoscope user interface prior to starting up.
- To run Caryoscope in "batch mode" in the background, to generate a graphics output file representing the data. In this way, Caryoscope could be used as part of a Web application.
Caryoscope is invoked from the command line as follows:
java -jar caryoscope-run.jar [options]
where we assume that you have the java command on your path, and that caryoscope-run.jar is in the current directory. The options you can specify are:
- -axisLineColor <#rrggbb>
See Section 3.2.2, “Axis line color” and Section 3.6.2, “Specifying colors in hexadecimal format”.
- -axisLineThickness <number>
- -batchMode
Whether to process the data in batch mode. If this option is not specified, Caryoscope will start up as an interactive application, and the -outputFile and -outputFormat options will be ignored.
- -centromereShown
- -chromosomeAxisShown
- -dataScaleIncrement <number>
- -dataScaleShown
- -displaySize <widthXheight>
Size in pixels of the Caryoscope display.
- -help
Causes Caryoscope to print a summary of command line options and exit. All other options are ignored.
- -inputFile <fileName>
Name of data input file. Based on the name of the file (*.gff, *.txt or *.csv), Caryoscope will infer that this file is in GFF format (see Section 3.4.1, “General Feature Format”), or tab- or comma-delimited spreadsheet format (see Section 3.4.2, “Spreadsheet-compatible text”), respectively.
- -listFormats
Causes Caryoscope to print a list of supported graphics output formats and exit. All other options are ignored. See the -outputFormat option.
- -logarithmBase <number>
- -logarithmEnabled
- -minimumFeatureWidth <number>
- -movingAverageEnabled
- -movingAverageHalfDecayDistance <integer>
- -movingAverageHalfWindowWidth <integer>
- -negativeValueColor <#rrggbb>
See Section 3.2.16, “Negative value color” and Section 3.6.2, “Specifying colors in hexadecimal format”.
- -outputFile <fileName>
Name of the graphics output file generated.
- -outputFormat <formatName>
Graphics output file format. See the -listFormats option.
- -positiveValueColor <#rrggbb>
See Section 3.2.17, “Positive value color” and Section 3.6.2, “Specifying colors in hexadecimal format”.
- -scaleLineColor <#rrggbb>
See Section 3.2.18, “Scale line color” and Section 3.6.2, “Specifying colors in hexadecimal format”.
- -scaleLineThickness <number>
- -viewBackgroundColor <#rrggbb>
See Section 3.2.20, “View background color” and Section 3.6.2, “Specifying colors in hexadecimal format”.
- -visibleDataset <datasetName>
The name of the dataset to display.