[galaxy-dev] Tool shed and tools with dynamically generated select list parameters
Hi, 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 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 I created their minus '.sample' versions in the same locations and added my local references to this lastz_seqs.loc, still nothing. I finally manually edited the main tool_data_table_conf.xml adding: !-- Locations of 2bit sequence files for use in Lastz -- table name=lastz_seqs comment_char=# columnsvalue, name, path/columns file path=tool-data/lastz_seqs.loc / /table And that did the trick. Is this the expected way of handling these cases?. 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 Galaxy instance. 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Tool shed and tools with dynamically generated select list parameters
Hello Carlos, On Jan 28, 2013, at 5:13 PM, Carlos Borroto wrote: Hi, 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 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 I created their minus '.sample' versions in the same locations and added my local references to this lastz_seqs.loc, still nothing. I finally manually edited the main tool_data_table_conf.xml adding: !-- Locations of 2bit sequence files for use in Lastz -- table name=lastz_seqs comment_char=# columnsvalue, name, path/columns file path=tool-data/lastz_seqs.loc / /table 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 interface, this should all happen automatically for you. If you download the repository as a tar archive and manually install it from outside of the Galaxy interface, you'll have to do all of this manually. 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 that require a missing entry in the tool_data_table_conf.xml file, this file will be modified in real time by adding the entry from a tool_data_table_conf.xml.sample file contained in the tool shed repository. Galaxy instance. 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: http://lists.bx.psu.edu/ ___ 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/
Re: [galaxy-dev] Tool shed and tools with dynamically generated select list parameters
On Mon, Jan 28, 2013 at 5:29 PM, Greg Von Kuster g...@bx.psu.edu wrote: 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 interface, this should all happen automatically for you. If you download the repository as a tar archive and manually install it from outside of the Galaxy interface, you'll have to do all of this manually. I guess I overwrote the main tool_data_table_conf.xml with the sample one at some point, cause I don't remember installing this repository manually. The next paragraph in the same wiki page clarifies this: For those tools that include dynamically generated select list parameters that require a missing entry in the tool_data_table_conf.xml file, this file will be modified in real time by adding the entry from a tool_data_table_conf.xml.sample file contained in the tool shed repository. Ooops, I stopped reading too soon. Thanks, 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: http://lists.bx.psu.edu/
