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.
Greg Von Kuster
On Fri, Nov 9, 2012 at 2:10 AM, Greg Von Kuster <greg(a)bx.psu.edu> wrote:
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.
> 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?
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