X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Ffeatures%2Fcommandline.html;h=0e1f10975ea3b345df16a88c8149b8e4cc23eaa1;hb=5ae33a27065b5bf32541bda82c295c2e12e2f76a;hp=cbe5a1c6c5cee6f187cc1f7e9dda1257264cb679;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git diff --git a/help/html/features/commandline.html b/help/html/features/commandline.html index cbe5a1c..0e1f109 100644 --- a/help/html/features/commandline.html +++ b/help/html/features/commandline.html @@ -1,52 +1,65 @@ -
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.
--
- - +
+ 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. +
++
+