For issue 1), so I think it's safe to remove the
& tool-data/tool_data_table_conf.xml.sample since they are not used?
For issue 2) if the galaxy will automatically pick up the new file
without configuring the ini file? Also how does this change affect the
existing shed tools like BWA that is using tool_data_table_conf.xml?
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
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
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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