X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fcommandline.html;fp=help%2Fhelp%2Fhtml%2Ffeatures%2Fcommandline.html;h=27a1a682935133281e9b14539f66b5160869d692;hb=e086b0c30bee5fe084186c65ef1ded42c58560f9;hp=92d9323e8fc36c3bbab96e30462084c55c731c0a;hpb=e51f922b88b1f316e27cf4c19eef437ff592d74d;p=jalview.git diff --git a/help/help/html/features/commandline.html b/help/help/html/features/commandline.html index 92d9323..27a1a68 100644 --- a/help/help/html/features/commandline.html +++ b/help/help/html/features/commandline.html @@ -26,38 +26,48 @@
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 + Jalview can be run from the command line, and provides a range of arguments. These arguments + can also be passed via .JVL files, which are opened + automatically by the Jalview application when double-clicked in a + file browser on Windows and OSX.
+ The way that you launch Jalview from the command line depends on the + platform you are on, and how it has been installed. + ++ /PATH_TO_JALVIEW/Jalview -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal+
+ \PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa+
+open /Applications/Jalview.app --args -open ~/myalignment.fa(put + all the Jalview arguments after the --args parameter) +
+ <Path to Java home>/bin/java -jar %lt;Path to Jalview Jar>/jalview-all-1.8.jar -open myalignment.fa
- 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 all the jar files in the
- Jalview installation's 'lib' directory to the classpath, as well as
- the Jalview application jar file:
+ If you have installed Jalview via conda or another package
+ manager then you most likely have a 'jalview' command available in
+ your terminal shell's default path. Alternately, if you have built
+ Jalview from source, then take a look at the doc/building.md file
+ included in the source distribution.
java -classpath "$INSTALL_DIR$/lib/*:$INSTALL_DIR$/jalview.jar" jalview.bin.Jalview -open [FILE]
Use '-help' to get more information on the command line arguments that - Jalview accepts. + href="clarguments.html">command line arguments that Jalview + accepts. +
+
+ Passing JVM Arguments to Jalview
If you need
+ to modify parameters for Jalview's Java Virtual Machine, then take a
+ look at the instructions for how to setting
+ the JVM's maximum memory.