From 713c09ec2d6f35d74ba2c6ed114bb3a29f3f5cf5 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 9 Feb 2007 18:02:17 +0000 Subject: [PATCH] running jalview from the command line. --- help/html/features/clarguments.html | 82 +++++++++++++++++++++++++++++++++++ help/html/features/commandline.html | 35 +++++++++++++++ 2 files changed, 117 insertions(+) create mode 100644 help/html/features/clarguments.html create mode 100644 help/html/features/commandline.html diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html new file mode 100644 index 0000000..45dfab5 --- /dev/null +++ b/help/html/features/clarguments.html @@ -0,0 +1,82 @@ + +Jalview Command Line Arguments + + +

The Jalview Executable's Command Line + Arguments

+ See running Jalview from the command + line for more information.
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
-nodisplay
Run Jalview without User Interface.
-props FILE
Use the given Jalview properties file instead + of users default.
-features FILE
+

Use the given file to add sequence features to an alignment. + See Features + File (Known as Groups file prior to 2.08) description.

+ +
-annotations FILE
Add precalculated annotations to the alignment. See Annotation + File description.
-fasta FILE
Create alignment file FILE in Fasta format.
-clustal FILE
Create alignment file FILE in Clustal format.
-msf FILE
Create alignment file FILE in MSF format.
-pileup FILE
Create alignment file FILE in Pileup format.
-pir FILE
Create alignment file FILE in PIR format.
-blc FILE
Create alignment file FILE in BLC format.
-jalview FILE
Create alignment file FILE in Jalview format.
-png FILE
Create PNG image FILE from alignment.
-imgMap FILE
Create HTML file FILE with image map of PNG + image.
-eps FILE
Create EPS file FILE from alignment.
+ + diff --git a/help/html/features/commandline.html b/help/html/features/commandline.html new file mode 100644 index 0000000..fadddce --- /dev/null +++ b/help/html/features/commandline.html @@ -0,0 +1,35 @@ + +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.

+

 

+

 

+ + -- 1.7.10.2