This error (and others like it) is raised when an old version of the Jalview Webstart JNLP is being used to launch the latest version of the application (for instance, because you have created your own JNLP file in order to increase the memory available to Jalview). If you are familiar with bug tracking systems, then you can register and submit a bug report directly to the Jalview Bug Tracker, otherwise, just send an email to the discussion mailing list describing the problem, and someone will take it from there. If you can reproduce the bug with a simpler data set, then send us that instead! Prepare a copy of the alignment file you are using when you find the bug, and try to describe as fully as possible the steps you took before the bug occurred. Prepare the input data and a description of how the bug is reproduced If you installed Jalview with InstallAnywhere, you will find a text file in the directory in which you installed Jalview called "output.txt" Include this file with any bug report you have.A Java console will be shown when Jalview starts up, and information about any problems should be output to the console window. Make sure you check the "Java Console" option to "Show Console", then click "OK" and restart Jalview. Then click the "Edit" menu, select "Preferences" then click the "Advanced" tab. If you installed Jalview using Java Webstart, locate and start the program "javaws" or "javaws.exe" on your system.
If it takes too long to reproduce your bug with the console open, then close it and try another way below:
#The java jar file cannot be launched mac free#
Check Jalview's memory settings ( Desktop->Tools->Show Memory usage) to make sure you have at least 50% memory free when testing this. Note: This FAQ has been updated - we no longer recommend the =lib argument since it prevents Jalview from accessing some web services, and will be disabled in future versions of Java.įirstly, see if you can reproduce the bug. The online documentation also includes a list of jalview command line parameters Use -help to list the current set of arguments Jalview supports. Where $INSTALL_DIR$ is the InstallAnywhere installation directory. Java -classpath "$INSTALL_DIR$/jalview.jar:$INSTALL_DIR$/lib/*" To use Jalview like a command line program from a terminal, we recommend you use the following command (you could also put this in a shell or batch script). However any output from the application will be sent to a file called output.txt in the directory where you installed Jalview, rather than to the command's standard output channel.ģ. If you installed the InstallAnywhere version of Jalview you can run the application binary with additional arguments. This is fine for launching the desktop with prepared data, but less useful for batch processing since any console output will be written to the java console.Ģ. If you use Java Web Start to launch Jalview, then on some versions of Java Webstart you can start up Jalview with a specific file by typing: The Jalview Desktop has a number of command line options, but how you access them depends on the way you want to launch Jalview:ġ.
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