Hello! Im looking for a way to run jar files(or class files) as a tool. Im not sure how to setup the galaxy instance to do this. For some reason i am running into a classpath issue. Anyone that could guide me in the right direction? Regards Frederick
Hi Frederick, I'm not an expert but maybe you could consider to write a python wrapper to call your Java application. --- Marco On 7 May 2011 08:08, Frederick van Staden <cmptrwizard@gmail.com> wrote:
Hello!
Im looking for a way to run jar files(or class files) as a tool. Im not sure how to setup the galaxy instance to do this. For some reason i am running into a classpath issue.
Anyone that could guide me in the right direction?
Regards Frederick
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Hi Fredrick, Writing python wraper for this purpose works and JPype should be used for calling java(class files) from python. Our team at UGA has developed a tool based on java and python for invoking REST Web services and we invoke the java class files in python using JPype. The tool has been uploaded to the community. Thanks, Chaitanya, University of Georgia. On Sat, May 7, 2011 at 4:46 AM, Marco Moretto <marco.moretto@gmail.com>wrote:
Hi Frederick, I'm not an expert but maybe you could consider to write a python wrapper to call your Java application.
--- Marco
On 7 May 2011 08:08, Frederick van Staden <cmptrwizard@gmail.com> wrote:
Hello!
Im looking for a way to run jar files(or class files) as a tool. Im not sure how to setup the galaxy instance to do this. For some reason i am running into a classpath issue.
Anyone that could guide me in the right direction?
Regards Frederick
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
There are a growing number of tools based on java packages - perhaps the example in tools/sr_mapping/srma_wrapper.xml could be a useful 'simple' starting point? For more complex scenarios, there are a number of new Picard based java tools (only exposed on test at present) in the galaxy-central source tree under tools/picard that do even more complex integration of multiple outputs into html output files. The relevant jars are all placed in tool-data/shared/jars and that path is passed in the xml command template as something like: --jar="${GALAXY_DATA_INDEX_DIR}/shared/jars/foo.jar" Of course YMMV depending on your specific needs but this approach certainly can be made to work for java packages like Picard and FastQC. On Sat, May 7, 2011 at 2:08 AM, Frederick van Staden <cmptrwizard@gmail.com>wrote:
Hello!
Im looking for a way to run jar files(or class files) as a tool. Im not sure how to setup the galaxy instance to do this. For some reason i am running into a classpath issue.
Anyone that could guide me in the right direction?
Regards Frederick
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
participants (4)
-
chaitanya guttula -
Frederick van Staden -
Marco Moretto -
Ross