Re: [galaxy-dev] Galaxy tools written in java
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 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] adding to the wiki
Is there a way i can contribute to the wiki? Regards Fred ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy tools written in java
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.more...@gmail.comwrote: 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 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy tools written in java
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
cmptrwiz...@gmail.comwrote:
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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--
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;
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Re: [galaxy-dev] Megablast GIs
On Saturday, May 7, 2011, drho...@uark.edu wrote: Thanks Peter, I debated which to post to. This is just using the Megablast tool in Galaxy. My IT people are not Biologists. They had this working fine and some tweak has screwed up the GI column in the results file. It should be the same NR and HTGS datafiles that we had before. So you recommend that I should just have them reinstall the databases and make sure to use the correct switches? You don't know what tweak broke things? You've got at least three factors, (1) Galaxy and the wrapper, but I don't see how an update of these would have affected the IDs. (2) The BLAST command line tool (blast all in this case), perhaps it was updated and this has altered the output? (3) The BLAST database(s) were updated (or rebuilt if you have local databases, in which case it could have been done with a newer version of the formatdb tool). If you are using NR does you have it regularly updated from the NCBI FTP site? Hopefully your admin team will have some sort of log of system updates that might help work out what happened. Peter ___ 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: http://lists.bx.psu.edu/
