X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fcommandline.html;h=9cffc515bc171e1bffb75af7676e1645641b859c;hb=74f810edbb5063639a53e4f34f7bb8e74235c4ef;hp=dd6c0de3c78fc09432a3fd7cd33e7b729dd67126;hpb=0943de76f6a7435894e72479671642c05f2f3687;p=jalview.git
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* along with Jalview. If not, see
Running Jalview from the command line
-Jalview is most easily run from the command line if you have built - it from source, or via the 'Jalview' executable created from the - InstallAnywhere Jalview installation. Both of these mechanisms allow - true command line execution of Jalview - allowing you to provide - additional options.
-The Java Webstart version of - Jalview can be executed from the command line using something like - : -
javaws http://www.jalview.org/webstart/jalview.jnlp -open - yourFileName- But, this is not guaranteed to work on all versions of webstart on all - operating systems, and doesn't let you execute Jalview with any - additional parameters. -
Running Jalview from the InstallAnywhere - installation
-If you install with InstallAnywhere you can use several more commands.
- However, if you call the application with the link provided by InstallAnywhere
- any output from the application will be sent to output.txt, not standard
- out.
- The Jalview application also requires a number of additional
- libraries on the class path. The command line below adds the Jalview
- installation's 'lib' directory to the list of directories that are
- searched for jars to be added to the classpath:
java -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -open [FILE]-
Use '-help' to get more information on the command line arguments that Jalview - accepts.
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- -