Melissa,
You can find additional examples in the following repository:
https://toolshed.g2.bx.psu.edu/view/devteam/package_picard_1_56_0
Which is then sourced by the following two repositories:
https://toolshed.g2.bx.psu.edu/view/devteam/picard
https://toolshed.g2.bx.psu.edu/view/devteam/sam_merge
--Dave B.
On 2014-08-30 08:13, Lukasse, Pieter wrote:
Hi Melissa,
See also
https://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_masscomb
or
https://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_proteomics
Regards,
Pieter.
-----Original Message-----
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Peter Cock
Sent: zaterdag 30 augustus 2014 4:32
To: Melissa Cline
Cc: Galaxy Dev
Subject: Re: [galaxy-dev] Examples of Galaxy tools in the toolsheds that
install and run JAR files properly?
On Sat, Aug 30, 2014 at 11:17 AM, Melissa Cline <cl...@soe.ucsc.edu> wrote:
Hi folks,
I'm attempting something that should be straightforward, but it's not.
I have a tool that runs a JAR file, which I have bundled with the
tool. I simply want to run the JAR file. And to paraphrase Thomas
Edison, I've tried several thousand things that do not work (at least
for me), from setting the JAVA_JAR_PATH environment variable in the
tool_dependencies.xml file to trying to copy the JAR file into the
tool-data/shared/jars subdirectories (which is the closest thing I've
got to working). So, at long last I'm doing the sensible thing and
looking for one simple working example that I can use as a template.
Who can suggest a good toolshed tool (either main or test) that
involves running its own JAR file, and that works?
Thanks!
Melissa
Here are a couple of my wrappers for Java tools, but I would suggest you invoke
the Java script with an absolute path to the JAR file:
$ java -jar ...
Here is two examples done via a Python wrapper script (mainly used for pre or
post processing the data files):
https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go
For EffectiveT3 which is open source and can therefore be easily redistributed,
I set an environment variable EFFECTIVET3 for the location of the Jar file,
which is used to invoke it via Java:
$ java -jar ...
For the Blast2GO wrapper, I require the person installing it setup an
environment variable B2G4PIPE pointing at the folder with the JAR file. Older
versions of this tool you be launched with the same -jar approach, but the
current release requires setting a class path instead:
$ java -cp ...
I hope that helps, if not there are bound to be other Java examples in the
ToolShed.
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
