From greg@bx.psu.edu Mon Jan 28 17:29:49 2013 From: Greg Von Kuster To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Tool shed and tools with dynamically generated select list parameters Date: Mon, 28 Jan 2013 17:29:45 -0500 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============3419869581929388177==" --===============3419869581929388177== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hello Carlos, On Jan 28, 2013, at 5:13 PM, Carlos Borroto wrote: > Hi, >=20 > I'm trying to get lastz to show a locally cached reference. As I'm > used to do I went ahead and copy tool-data/lastz_seqs.loc.sample(still > included with galaxy-dist) to tool-data/lastz_seqs.loc and added my > local references. Nothing happened. I get: > galaxy.tools.parameters.dynamic_options WARNING 2013-01-28 > 16:42:58,203 Data table named 'lastz_seqs' is required by tool but not > configured >=20 > I realized there are these two files in the lastz repository: > ../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/lastz/0801f8207d30/lastz= /tool_data_table_conf.xml.sample > ../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/lastz/0801f8207d30/lastz= /tool-data/lastz_seqs.loc.sample >=20 > I created their minus '.sample' versions in the same locations and > added my local references to this lastz_seqs.loc, still nothing. >=20 > I finally manually edited the main tool_data_table_conf.xml adding: > > > value, name, path > >
>=20 > And that did the trick. Is this the expected way of handling these cases?. Yes, however, if your install the repository from the Galaxy administrator in= terface, this should all happen automatically for you. If you download the r= epository as a tar archive and manually install it from outside of the Galaxy interface, you'll have to = do all of this manually. >=20 > This paragraph from the wiki didn't clarify much for me: > http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy > "Tool shed repositories that contain tools that include dynamically > generated select list parameters that refer to an entry in the > tool_data_table_conf.xml file must contain a > tool_data_table_conf.xml.sample file that contains the required entry > for each dynamic parameter. Similarly, any index files (i.e., > ~/tool-data/xxx.loc files) to which the tool_data_table_conf.xml file > entries refer must be defined in xxx.loc.sample files included in the > tool shed repository along with the tools. If any of these > tool_data_table_conf.xml entries or any of the required xxx.loc.sample > files are missing from the tool shed repository, the tools will not > properly load and metadata will not be generated for the repository. > This means that the tools cannot be automatically installed into a The next paragraph in the same wiki page clarifies this: For those tools that include dynamically generated select list parameters tha= t require a missing entry in the tool_data_table_conf.xml file, this file wil= l be modified in real time by adding the entry from a tool_data_table_conf.xm= l.sample file contained in the tool shed repository. > Galaxy instance." >=20 > Best regards, > Carlos > ___________________________________________________________ > 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: >=20 > http://lists.bx.psu.edu/ --===============3419869581929388177== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 PGh0bWw+PGhlYWQ+PC9oZWFkPjxib2R5IHN0eWxlPSJ3b3JkLXdyYXA6IGJyZWFrLXdvcmQ7IC13 ZWJraXQtbmJzcC1tb2RlOiBzcGFjZTsgLXdlYmtpdC1saW5lLWJyZWFrOiBhZnRlci13aGl0ZS1z cGFjZTsgIj5IZWxsbyBDYXJsb3MsPGRpdj48YnI+PGRpdj48ZGl2Pk9uIEphbiAyOCwgMjAxMywg YXQgNToxMyBQTSwgQ2FybG9zIEJvcnJvdG8gd3JvdGU6PC9kaXY+PGJyIGNsYXNzPSJBcHBsZS1p bnRlcmNoYW5nZS1uZXdsaW5lIj48YmxvY2txdW90ZSB0eXBlPSJjaXRlIj48ZGl2PkhpLDxicj48 YnI+SSdtIHRyeWluZyB0byBnZXQgbGFzdHogdG8gc2hvdyBhIGxvY2FsbHkgY2FjaGVkIHJlZmVy ZW5jZS4gQXMgSSdtPGJyPnVzZWQgdG8gZG8gSSB3ZW50IGFoZWFkIGFuZCBjb3B5IHRvb2wtZGF0 YS9sYXN0el9zZXFzLmxvYy5zYW1wbGUoc3RpbGw8YnI+aW5jbHVkZWQgd2l0aCBnYWxheHktZGlz dCkgdG8gdG9vbC1kYXRhL2xhc3R6X3NlcXMubG9jIGFuZCBhZGRlZCBteTxicj5sb2NhbCByZWZl 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