Fantastic! Thanks for all the details Greg.

Cheers,
Derrick


On Fri, Nov 9, 2012 at 10:55 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:

> Hi Derrick,
>
> On Nov 9, 2012, at 12:56 AM, Derrick Lin wrote:
>
> For issue 1), so I think it's safe to remove the 
> tool-data/tool_data_table_conf.xml
> & tool-data/tool_data_table_conf.xml.sample since they are not used?
>
>
>
> Yes, the ~/tool-data/tool_data_table_conf.xml.sample and
> ~/tool-data/tool_data_table_conf.xml.sample files can be removed.
>
>
>
> For issue 2) if the galaxy will automatically pick up the new file 
> shed_tool_data_table_conf.xml
> without configuring the ini file?
>
>
> Yes, no changes are necessarey in your universe_wsgi.ini file unless you
> want to name these particular files differently than these default names.
>  The change set I committed includes entries in universe_wsgi.ini.sample
> for both of these files (the tool_data_table_conf.xml file was never added
> to the sample ini), but adding the new settings to the universe_wsgi.ini
> file is not required as the default names will be used.
>
>
> Also how does this change affect the existing shed tools like BWA that is
> using tool_data_table_conf.xml?
>
>
> The existing shed tools will contiue to function as usual, but entries for
> them will be in the tool_data_table_conf.xml file.  ANy new tools installed
> from the tool shed that use entries like this will be added to the new
> shed_tool_data_table_conf.xml file.  Entries from both of these files are
> loaded into the ToolDataTableManager.  The intent is for the Galaxy admin
> to be able to manuall make changes to the tool_data_table_conf.xml file and
> not have them munged by the tool shed's installation process.  This is the
> same approach used for the tool_conf.xml file, where the Galaxy tool shed
> repository installation process uses the shed_tool_conf.xml file.
>
> Thanks Derrick,
>
> Greg Von Kuster
>
>
> Cheers,
> D
>
>
> On Fri, Nov 9, 2012 at 2:10 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>
>> Hello Derrick,
>>
>> Your message discusses 2 separate issues:
>>
>> 1. When you install your meme_chip repository from the tool shed, the
>> file named tool_data_table_conf.xml.sample contained in the repository is
>> copied to the ~/tool-data directory in the local Galaxy instance.  This
>> issue has been corrected in change set b5ce9451c5d1 which I committed this
>> morning to the galaxy-central repository.
>>
>> 2. When you install your meme_chip repository from the tool shed, the
>> entries defined in the file named tool_data_table_conf.xml.sample contained
>> in the repository are not entered into the tool_data_table_conf.xml file in
>> the local Galaxy instance.  This issue was corrected in change
>> set bc5fa254bafc which I committed to the galaxy-central repository
>> yesterday.  With this change set, entries for data tables that are defined
>> in tool_data_table_conf.xml.sample files included in the tool shed
>> repository will be automatically added to a new separate file named
>> shed_tool_data_table_conf.xml.  This will ensure that manual edits made to
>> the original tool_data_table_conf.xml file will not be munged when Galaxy's
>> tool shed repository installation process automatically adds entries into
>> the file.
>>
>> Unfortunately both of these fixes have not made it into the Galaxy
>> release that is currently planned for this week, so they will be available
>> in the release currently scheduled for 2 weeks from now.
>>
>> Thanks very much for reporting both of these issues, and sorry for the
>> inconvenience they may have caused.
>>
>> Greg Von Kuster
>>
>>
>> On Nov 7, 2012, at 8:19 PM, Derrick Lin wrote:
>>
>> It's actually in related to a new galaxy shed tool we developed called
>> meme-chip, we uploaded it to the main Tool Shed site.
>>
>> We provided tool_data_table_conf.xml.sample and xxx.loc.sample  along
>> with the tool. After the installation, the loc file has been populated
>> automatically, but the entry inside tool_data_table_conf.xml.sample
>> didn't get populated.
>>
>> Although it can be fixed easily by adding entries to the runtime 
>> tool_data_table_conf.xml
>> manually, it's good to know if it's the right way or we are missing
>> something in the shed tool repos.
>>
>> Cheers,
>> D
>>
>>
>> On Thu, Nov 8, 2012 at 10:20 AM, Derrick Lin <klin...@gmail.com> wrote:
>>
>>> Hi guys,
>>>
>>> After installing the BWA from the Tools Shed, I find there is a
>>> new tool_data_table_conf.xml got created under tool-data directory. The
>>> file contains the entries of BWA's loc files.
>>>
>>> I believe the installed BWA still relies on the tool_data_table_conf.xml
>>> under galaxy root dir. Anyone can clarify what the one under tool-data dir
>>> is for?
>>>
>>> Regards,
>>> Derrick
>>>
>>
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>>
>
>
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