Re: [galaxy-dev] A new tool_data_table_conf.xml created under tool-data directory

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&gt; 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&gt; 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 >> > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > >