Hi,
In the past, I've done something like this:
<command> #set $jar_dir = "/mydir/jars/" java -cp $jar_dir/my_jar.jar:$jar_dir/my_second_jar.jar MyClass $input </command>
However, it looks like you can set a jar directory. Here's the relevant bit from a recent update:
4) Add a jar directory / bin which is accessible to tool configurations by specifying e.g. '${GALAXY_DATA_INDEX_DIR}/shared/jars/FOO.jar', where FOO.jar is the desired jar which has been placed in / linked to 'GALAXY_ROOT/tool-data/shared/jars' (by default; $GALAXY_DATA_INDEX_DIR can be configured to point elsewhere [value of 'tool_data_path' configuration variable in universe_wsgi.ini]). The setup.sh script has been modified to create this directory when not present.
I haven't tried using this, so I'm not entirely sure how a tool would use a jar in the shared directory.
On Fri, Jun 18, 2010 at 7:40 AM, Elie Freilich Elie.Freilich@gmail.com wrote:
Hello,
I just started working with developing a tool for Galaxy; I have been programming it in Java. However, when it came time to implement my tool into Galaxy, I was unable. When I try to run it normally, it works. However, in Galaxy, when I try to use the JAR file, it produces a java.lang.NoClassDefFoundError and a java.lang.ClassNotFoundException.
As it seems rather meaningless to be setting a classpath in an abstract framework like Galaxy, is there a simple way to run Java JAR files? I tried a "-jar" argument, but I can't put in an argument before the filename. Should I be using the ".class" files instead of the JAR files? Should the format in the XML file be <command interpreter="java"></command>?
Thanks so much, Elie _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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