On Jan 28, 2013, at 5:13 PM, Carlos Borroto wrote:

Hi,

I'm trying to get lastz to show a locally cached reference. As I'm
used to do I went ahead and copy tool-data/lastz_seqs.loc.sample(still
included with galaxy-dist) to tool-data/lastz_seqs.loc and added my
local references. Nothing happened. I get:
galaxy.tools.parameters.dynamic_options WARNING 2013-01-28
16:42:58,203 Data table named 'lastz_seqs' is required by tool but not
configured

I realized there are these two files in the lastz repository:
../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/lastz/0801f8207d30/lastz/tool_data_table_conf.xml.sample
../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/lastz/0801f8207d30/lastz/tool-data/lastz_seqs.loc.sample

I created their minus '.sample' versions in the same locations and
added my local references to this lastz_seqs.loc, still nothing.

I finally manually edited the main tool_data_table_conf.xml adding:
   
   <table name="lastz_seqs" comment_char="#">
       <columns>value, name, path</columns>
       <file path="tool-data/lastz_seqs.loc" />
   </table>

And that did the trick. Is this the expected way of handling these cases?.

Yes, however, if your install the repository from the Galaxy administrator interface, this should all happen automatically for you. If you download the repository as a tar archive

and manually install it from outside of the Galaxy interface, you'll have to do all of this manually.

This paragraph from the wiki didn't clarify much for me:
http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy
"Tool shed repositories that contain tools that include dynamically
generated select list parameters that refer to an entry in the
tool_data_table_conf.xml file must contain a
tool_data_table_conf.xml.sample file that contains the required entry
for each dynamic parameter. Similarly, any index files (i.e.,
~/tool-data/xxx.loc files) to which the tool_data_table_conf.xml file
entries refer must be defined in xxx.loc.sample files included in the
tool shed repository along with the tools. If any of these
tool_data_table_conf.xml entries or any of the required xxx.loc.sample
files are missing from the tool shed repository, the tools will not
properly load and metadata will not be generated for the repository.
This means that the tools cannot be automatically installed into a

The next paragraph in the same wiki page clarifies this:

For those tools that include dynamically generated select list parameters that require a missing entry in the tool_data_table_conf.xml file, this file will be modified in real time by adding the entry from a tool_data_table_conf.xml.sample file contained in the tool shed repository.

Galaxy instance."

Best regards,
Carlos
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