Yay, with your tip, galaxy direct tests now work with tool_conf.xml AND data table in place!
Galaxy DOC person: please update https://wiki.galaxyproject.org/Admin/RunningTests to state that tool_conf.xml.sample is NOT used for testing! It is stated in the run_tests.sh help info half way down the page. Tool wasn't loading on new site because data table it referenced wasn't set up. I'll note for galaxy devs that the WARNING is actually fatal i.e. that missing data table caused some kind of weird error: galaxy.tools.toolbox.base INFO 2015-02-27 13:48:48,190 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.parameters.dynamic_options WARNING 2015-02-27 13:48:48,199 Data table named 'blast_reporting_fields' is required by tool but not configured galaxy.tools.toolbox.base ERROR 2015-02-27 13:48:48,200 Error reading tool from path: TESTING/blast_reporting/blast_reporting.xml Traceback (most recent call last): File "...galaxy-dist/lib/galaxy/tools/toolbox/base.py", line 670, in _load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) ... File ".../galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 608, in column_spec_to_index return int( column_spec ) ValueError: invalid literal for int() with base 10: 'type' Thanks again, Peter! Damion Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ________________________________________ From: Peter Cock [p.j.a.c...@googlemail.com] Sent: Friday, February 27, 2015 1:39 PM To: Dooley, Damion Cc: galaxy-...@lists.bx.psu.edu Subject: Re: Tool Testing: field inputs that occur inside repeat tag - semi resolved. ... > And I run "tests.sh -id blast_reporting" (with Galaxy as owner > of tool folder): While the tests used to use tool_conf.xml.sample last year (or even longer ago?) this was switched to using the main tool_conf.xml instead. This is much easier for testing what you actually have installed. If I've guessed wrong, watch the run_tests.sh output to see which tools are loaded - and make sure your tool loads OK (and for example doesn't fail with an XML error or something). Peter ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
