Fantastic! Thanks for all the details Greg.
Cheers,
Derrick
On Fri, Nov 9, 2012 at 10:55 PM, Greg Von Kuster <greg(a)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 <greg(a)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 <klin938(a)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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