Tool not showing up
Hi All, I've created a new tool but I'm unable to get it to show up under "My Tools". I've added it to tool_conf.xml, as shown here: http://codepad.org/sJHNzabY And my tool configuration can be viewed here: http://codepad.org/9r4tnNYV The only tool that shows up under My Tools is soap2. I've confirmed that both the tools/macs folder and macs.xml itself are owned by the Galaxy user. I've tried in several different browsers in case it was a caching issue, but that doesn't seem to be it either. Any ideas? Cheers -- Branden Timm Great Lakes Bioenergy Research Center btimm@glbrc.wisc.edu
Hi Branden, When you start up Galaxy check the log, you will see the messages as it's loading all the tools and if a tool doesn't show up it is very likely there is a problem with its xml file and you will see the error message in the server log. leandro On Wed, Sep 1, 2010 at 11:46 PM, Branden Timm <btimm@wisc.edu> wrote:
Hi All, I've created a new tool but I'm unable to get it to show up under "My Tools". I've added it to tool_conf.xml, as shown here: http://codepad.org/sJHNzabY And my tool configuration can be viewed here: http://codepad.org/9r4tnNYV The only tool that shows up under My Tools is soap2. I've confirmed that both the tools/macs folder and macs.xml itself are owned by the Galaxy user. I've tried in several different browsers in case it was a caching issue, but that doesn't seem to be it either. Any ideas?
Cheers
-- Branden Timm Great Lakes Bioenergy Research Center btimm@glbrc.wisc.edu _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Indeed, there is a problem indicated in Paster but I'm not sure what the traceback is telling me. galaxy.tools ERROR 2010-09-01 17:00:22,238 error reading tool from path: macs/macs.xml Traceback (most recent call last): File "/home/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 74, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/home/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 141, in load_tool return ToolClass( config_file, root, self.app ) File "/home/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 282, in __init__ self.parse( root ) File "/home/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 375, in parse self.parse_inputs( root ) File "/home/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 460, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/home/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 599, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/home/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 679, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/home/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 689, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/home/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py", line 148, in build return parameter_types[param_type]( tool, param ) File "/home/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py", line 200, in __init__ raise ValueError( "The settings for this field require a 'value' setting and optionally a default value which must be an integer" ) ValueError: The settings for this field require a 'value' setting and optionally a default value which must be an integer Leandro Hermida wrote:
Hi Branden,
When you start up Galaxy check the log, you will see the messages as it's loading all the tools and if a tool doesn't show up it is very likely there is a problem with its xml file and you will see the error message in the server log.
leandro
On Wed, Sep 1, 2010 at 11:46 PM, Branden Timm <btimm@wisc.edu> wrote:
Hi All, I've created a new tool but I'm unable to get it to show up under "My Tools". I've added it to tool_conf.xml, as shown here: http://codepad.org/sJHNzabY And my tool configuration can be viewed here: http://codepad.org/9r4tnNYV The only tool that shows up under My Tools is soap2. I've confirmed that both the tools/macs folder and macs.xml itself are owned by the Galaxy user. I've tried in several different browsers in case it was a caching issue, but that doesn't seem to be it either. Any ideas?
Cheers
-- Branden Timm Great Lakes Bioenergy Research Center btimm@glbrc.wisc.edu _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hm, ok so I had an integer parameter with no "value" set. Setting a value there did allow the tool to load. Why is it that integer params require a default value? The parameter is for genome size where, at least in my opinion, it doesn't make great sense to set a default value. -- Branden Timm Great Lakes Bioenergy Research Center btimm@glbrc.wisc.edu Leandro Hermida wrote:
Hi Branden,
When you start up Galaxy check the log, you will see the messages as it's loading all the tools and if a tool doesn't show up it is very likely there is a problem with its xml file and you will see the error message in the server log.
leandro
On Wed, Sep 1, 2010 at 11:46 PM, Branden Timm <btimm@wisc.edu> wrote:
Hi All, I've created a new tool but I'm unable to get it to show up under "My Tools". I've added it to tool_conf.xml, as shown here: http://codepad.org/sJHNzabY And my tool configuration can be viewed here: http://codepad.org/9r4tnNYV The only tool that shows up under My Tools is soap2. I've confirmed that both the tools/macs folder and macs.xml itself are owned by the Galaxy user. I've tried in several different browsers in case it was a caching issue, but that doesn't seem to be it either. Any ideas?
Cheers
-- Branden Timm Great Lakes Bioenergy Research Center btimm@glbrc.wisc.edu _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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Leandro Hermida