Re: [galaxy-dev] Correct toolshed tool config for a .loc file
One further piece of the mystery I see now: The "View Data tables Registry" shows my tool's loc files, but has odd stuff for "Tool data path" and "Missing index file" columns, for example: blast_reporting_fields [tab] /usr/local/galaxy/test/galaxy-dist/tool-data/salk.bccdc.med.ubc.ca/toolshed/repos/ddooley/blast_reporting/00d397a381f8/blast_reporting_fields.loc [tab] /usr/local/galaxy/test/galaxy-dist/tool-data ./database/tmp/tmp-toolshed-gmfcrDITxyK/blast_reporting_fields.loc [tab] ./database/tmp/tmp-toolshed-gmfcrDITxyK [tab] missing There is no galaxy-dist/database/tmp-toolshed-gmfcrDITxyK folder, if that's where its supposed to be? Is there some setting for database tmp folder cache for tools? Thanks for tips ... Damion
So I see this now in main.log: galaxy.tools.data WARNING 2014-05-07 16:40:29,613 Line 3 in tool data table 'blast_reporting_fields' is invalid (HINT: '<TAB>' characters must be used to separate fields): length numeric int 1 1 1 Alignment length The thing is, tab characters ARE separating the fields. Its just that some columns don't have values. Now, this was working fine on the other galaxy install, updated to December 2013 changeset 11247 . So has .loc processing changed since then? Damion
Well Galaxians, I have to eat humble pie, kind of. Mismatches between the tool's tool_data_table_conf.xml and the actual tabular data were responsible for the disappearing act, which log rather indirectly alluded to. Something that didn't show itself on the dev server. I'll push for some greater reporting on this though, on the Trello board. What I'd like to see is the "View data tables registry" report have its "Missing index file" column changed to something like "Status" and under that you get to see "Missing index file" or Bad file - Parse error, 23 lines" etc. So my apologies to anyone who put some time into this. Damion
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Dooley, Damion