>> On Sep 12, 2012, at 1:00 PM, David Hoover wrote:
>>
>> Are there any environment variables that are honored by toolshed installed
>> tools? I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or
>> $GALAXY_HOME, then uploaded it the test toolshed, then installed it
>> automatically. Neither of these resolved to what I expected. I don't want
>> to hard-code the path in the xml tool file, but rather have a default
>> location for other executables and jar files. How should this best be done?
>>
>> David Hoover
>> Helix Systems Staff
On Wed, Sep 12, 2012 at 6:15 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> Hello David,
>
> This is not currently possible, but will be available in the next Galaxy
> distribution release, currently scheduled for about 10 days from now. You
> will include a tool_dependencies.xml file in your tool shed repository that
> looks something like the following.
>
> <?xml version="1.0"?>
> <tool_dependency>
> <set_environment version="1.0">
> <environment_variable name="JAVA_JAR_PATH"
> action="set_to">$INSTALL_DIR</environment_variable>
> </set_environment>
> </tool_dependency>
>
> Your tool will find the required files via the defined JAVA_JAR_PATH by
> using a <requirements> tag set in the tool config, something like this:
>
> <requirements>
> <requirement type="set_environment">JAVA_JAR_PATH </requirement>
> </requirements>
>
> The <command> tag in the tool config would be something like this:
>
> <command interpreter="python">
> python_wrapper.py $JAVA_JAR_PATH/some_file.jar $param1 $param2...
> </command>
>
> I'm close to having this working, so if you are interested in testing before
> the next Galaxy dist release, let me know and I'll tell you when the Galaxy
> central repository has the new feature.
>
> Thanks!
>
> Greg Von Kuster
Hi guys,
Reading the rest of the thread from December, Greg's new code did
get checked in and should be working (I've not tried this yet).
However, I can't help feeling that defining the two environment variables
David suggested, $GALAXY_DATA_INDEX_DIR and/or $GALAXY_HOME,
would cover the majority of use cases and be far simpler for tool authors
to use. Am I overlooking something?
Usecase: Tool comes with a simple datafile (e.g. defining a search motif,
say motif.dat) which is used by a script (say motif.py) via a normal
Galaxy tool XML file (say motif.xml).
Perhaps I can just put my data file next to the script and XML file, in
which case it is easy for the script to locate? But I assumed that
Galaxy best practice would be to use the tool-data folder somehow...
Thanks,
Peter
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