Running Phenote from the Command Line

1) Install Java 1.5 or higher

On Macs, Java 1.5 can be installed automatically by doing a system software update. On any other platform, download the appropriate binaries from the latest Java, currently JRE 6, http://java.sun.com/javase/downloads/index.jsp. To run Java applications, all you need is the JRE (Java Runtime Environment). If you need all the tools to run and create Java applications, download the J2SE SDK (Software Development Kit).

What version of Java do I have?

Most new computers come with some version of Java already installed. To figure out what version you have, open up a command prompt, or console, or terminal, or whatever you use on your platform to type commands onto a command-line. Then type:

java -version

and press enter. You should get a response like:

java version "1.5.0_06"
Java(TM) 2 Runtime Environment, 
Standard Edition (build 1.5.0_06-b05)
Java HotSpot(TM) Client VM (build 
1.5.0_06-b05, mixed mode, sharing)

The very first line tells you which version of Java is installed.

If you get a response like:

'java' is not recognized as an internal or external 
command, operable program or batch file.

bash: java: command not found

then check that you typed a space after "java" and before "-version". If you entered the command correctly but still do not get a response indicating a specific version of Java, then Java is not installed, and you need to follow the installation instructions above.

2) Get Phenote

The latest development version of Phenote can be retrieved from SourceForge.net Subversion repository through SVN with the following instruction set:

svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote

If you would like to check out a particular release, you will have to check out that particular version from the "tags" directory. For example, to checkout version 1.1 into your phenote1.1/ directory, you would use the following command:

svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.1/ phenote1.1

Information about accessing this Subversion repository may be found in a document titled "Subversion (Version Control for Source Code)".

3) Launch Phenote

On Unix platforms (including Mac OS), run the "phenote" shell script to start the program (to do this on most Unix platforms, change to the Phenote directory and type "./phenote").
On Windows or Mac, you can double-click the Phenote icon to launch the application.

4) Optional command-line arguments

When invoking Phenote from the command line, you can use one or more of these command-line options if you wish:

Options:
  -f, --inputFile=filename         Filename to read in 
  -w, --writeFile=filename         Filename to write to
  -c, --configSet=config file      Specify config file to use (should be a .cfg 
                                   file in conf directory).  (Note that this 
                                   change applies only to the current Phenote 
                                   session--the next time you launch Phenote, it
                                   will revert to your previously set 
                                   configuration.)
  -u, --updateConfig=config file   Specify config file to update from conf 
                                   directory.  Adds in new config fields; if 
                                   nothing to update just loads config file as 
                                   is.
  -l, --logFile=filename           Specify log file

  -?, --help                       Show this help message
  --usage                          Show brief usage message

So, for example,

phenote -c plant.cfg

would launch Phenote using the plant configuration, and

phenote -f data/mydatafile.tab

would bring up Phenote with the annotations in mydatafile.tab already loaded.