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 >> >> ___________________________________________________________ >> 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/ > >
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