[galaxy-dev] Correct toolshed tool config for a .loc file

2014-05-07 Thread Dooley, Damion 
I'll try to keep this short!  I'm wondering why on a fresh install of galaxy 
via a setup script into a python virtualenv, my custom toolshed tool's .loc 
files don't seem to be loading, i.e. the tool's tool_data_table_conf.xml file 
isn't loading.  All the other parts of the tool (and other toolshed tools) do 
run ok.  On the galaxy install where the tool was developed, it runs ok too, 
and I can't see any universe.wsgi.conf differences that would account for this 
though I'm sure the dev server has a number of other different config settings.

I thought I knew my way around this .loc stuff, but I'm flummoxed.  It is as 
though /usr/local/galaxy/test/galaxy-dist/tool-data/[toolshed domain etc 
etc]/00d397a381f8/tool_data_table_conf.xml isn't loading into Galaxy's tabular 
data list?!

The only other thing I can think of is that I stuffed the tool-data related loc 
files into a subfolder of the tool

   blast_reporting.py
   blast_reporting.xml
   tool_data_table_conf.xml.sample
   ...
   tool-data/
  blast_reporting_fields.loc.sample

But the resulting downloaded tool config in the galaxy-dist/tool-data/. 
/blast_reporting_fields.loc and tool_data_table_conf.xml files seem just fine!!!

Regards,

Damion
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Re: [galaxy-dev] Correct toolshed tool config for a .loc file

2014-05-07 Thread Dooley, Damion 
One further piece of the mystery I see now:

The View Data tables Registry shows my tool's loc files, but has odd stuff 
for Tool data path and Missing index file columns, for example:

   blast_reporting_fields [tab] 
/usr/local/galaxy/test/galaxy-dist/tool-data/salk.bccdc.med.ubc.ca/toolshed/repos/ddooley/blast_reporting/00d397a381f8/blast_reporting_fields.loc
 [tab] /usr/local/galaxy/test/galaxy-dist/tool-data

   ./database/tmp/tmp-toolshed-gmfcrDITxyK/blast_reporting_fields.loc [tab] 
./database/tmp/tmp-toolshed-gmfcrDITxyK [tab] missing

There is no galaxy-dist/database/tmp-toolshed-gmfcrDITxyK folder, if that's 
where its supposed to be? Is there some setting for database tmp folder cache 
for tools?

Thanks for tips ...

Damion
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