On Fri, Feb 15, 2013 at 4:05 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> 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
> The current implementation places your motif.dat data file in the
> repository installation directory, and tools that are properly configured
> to locate dependencies that are included in the repository contents
> will find it. This approach allows for tool dependency discovery and
> easy maintenance when uninstalling repositories as all contents are
> kept where they were installed.  Tools that are properly configured
> with <requirement> tags will find dependencies because the
> associated env.sh file is sourced, providing the location of all
> dependencies to the environment.

Is there a documented example I should be reading? In this use case
(without any explicit XML markup), can I assume/have the motif.dat
file be installed in the same folder next to the motif.py script and tool
defining motif.xml file?

> If your motif.dat file is one that would be manually altered by the
> Galaxy administrator over time, perhaps automatically moving it
> to the GALAXY_DATA_INDEX_DIR is justified.  However, in this
> case, uninstalling the repository would probably not uninstall the
> motif.dat file.  Does this fit with what you are thinking?

In this case no, I would not expect the motif.dat file to be edited.

Does this mean GALAXY_DATA_INDEX_DIR and the galaxy
tool-data folder are intended for 'configuration' files the local admin
may need to edit, rather than static tool specific data file?

> What kinds of files would require knowledge of the GALAXY_HOME
> directory?

Knowing GALAXY_DATA_INDEX_DIR would probably cover most
cases, so knowing GALAXY_HOME is probably not needed.


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