Re: [galaxy-dev] Galaxy tools written in java

2011-05-07 Thread Marco Moretto
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 cmptrwiz...@gmail.com wrote: Hello! Im looking for a way to run jar files(or class files) as a tool. Im not sure how to

Re: [galaxy-dev] Galaxy tools written in java

2011-05-07 Thread chaitanya guttula
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

Re: [galaxy-dev] Galaxy tools written in java

2011-05-07 Thread Ross
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