X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fcommandline.html;h=7b58a34cb5732f481526ce40586b71a4e7dd44ea;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=6c6f3ebff361659d30ede299b7924d354b3257d1;hpb=c53aeee9a688f68d64106a968876e542f701fbc6;p=jalview.git diff --git a/help/html/features/commandline.html b/help/html/features/commandline.html index 6c6f3eb..7b58a34 100644 --- a/help/html/features/commandline.html +++ b/help/html/features/commandline.html @@ -1,52 +1,65 @@ -Running Jalview from the command line + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> + +Running Jalview from the command line + -

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. +

+

 

+

 

+ +