[galaxy-dev] Few possible galaxy bugs ?
Good Morning, I am just in the process of updating our development galaxy, the following issues are been reported and I am unable to resolved them, would anyone have any suggestions. Just a little more background info, galaxy@jic55666:~/software/galaxy-central$ hg tip changeset: 6143:6c8695c2a949 tag: tip user:Greg Von Kuster date:Wed Oct 19 16:47:25 2011 -0400 summary: Enhanced Galaxy instance <=> Galaxy tool shed integration: galaxy@jic55666:~/software/galaxy-central$ python --version Python 2.6.6 the errors reported galaxy.tools DEBUG 2011-10-20 13:18:47,691 Loaded tool: hmmscan 1.0.0 docutils WARNING 2011-10-20 13:18:47,697 :2: (WARNING/2) Inline strong start-string without end-string. docutils WARNING 2011-10-20 13:18:47,700 :17: (ERROR/3) Unexpected indentation. galaxy.tools ERROR 2011-10-20 13:18:47,722 error reading tool from path: toolshed/nlstradamus/tools/protein_analysis/nlstradamus.txt Traceback (most recent call last): File "/home/galaxy/software/galaxy-central/lib/galaxy/tools/__init__.py", line 106, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/home/galaxy/software/galaxy-central/lib/galaxy/tools/__init__.py", line 186, in load_tool tree = util.parse_xml( config_file ) File "/home/galaxy/software/galaxy-central/lib/galaxy/util/__init__.py", line 105, in parse_xml tree = ElementTree.parse(fname) File "/home/galaxy/software/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/galaxy/software/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 583, in parse parser.feed(data) File "/home/galaxy/software/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 1242, in feed self._parser.Parse(data, 0) ExpatError: syntax error: line 1, column 0 galaxy.tools DEBUG 2011-10-20 13:18:50,172 Loaded tool: tophat 1.5.0 docutils WARNING 2011-10-20 13:18:50,208 :50: (WARNING/2) Literal block expected; none found. galaxy.tools.test DEBUG 2011-10-20 13:18:50,221 Error in add_param for min_coverage_intron: Unable to determine parameter type of test input 'min_coverage_intron'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2011-10-20 13:18:50,222 Error in add_param for max_coverage_intron: Unable to determine parameter type of test input 'max_coverage_intron'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools DEBUG 2011-10-20 13:18:50,222 Loaded tool: tophat_color 1.0.0 galaxy.tools DEBUG 2011-10-20 13:18:50,255 Loaded tool: cufflinks 0.0.5 galaxy.tools DEBUG 2011-10-20 13:18:50,428 Loaded tool: cuffcompare 0.0.5 galaxy.tools DEBUG 2011-10-20 13:18:50,462 Loaded tool: cuffdiff 0.0.5 galaxy.tools DEBUG 2011-10-20 13:18:51,301 Loaded tool: rgManQQ1 1.0.3 galaxy.tools.test DEBUG 2011-10-20 13:18:51,323 Error in add_param for force: Unable to determine parameter type of test input 'force'. Ensure that the parameter exists and that any container groups are defined first. = - Please note, that my email address is no longer givenname.surn...@bbsrc.ac.uk. Please update your records to reflect my new email address of givenname.surn...@nbi.ac.uk as shown on this email.___ 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] Few possible galaxy bugs ?
On Mon, Oct 24, 2011 at 11:17 AM, michael burrell (TOC) wrote: > Good Morning, I am just in the process of updating our development galaxy, > the following issues are been reported and I am unable to resolved them, > would anyone have any suggestions. > > Just a little more background info, > > galaxy@jic55666:~/software/galaxy-central$ hg tip > > changeset: 6143:6c8695c2a949 > tag: tip > user: Greg Von Kuster > date: Wed Oct 19 16:47:25 2011 -0400 > summary: Enhanced Galaxy instance <=> Galaxy tool shed integration: > > galaxy@jic55666:~/software/galaxy-central$ python --version > > Python 2.6.6 > > > > the errors reported…. > > > > > > galaxy.tools DEBUG 2011-10-20 13:18:47,691 Loaded tool: hmmscan 1.0.0 > > docutils WARNING 2011-10-20 13:18:47,697 :2: (WARNING/2) Inline > strong start-string without end-string. > > > > docutils WARNING 2011-10-20 13:18:47,700 :17: (ERROR/3) Unexpected > indentation. > > > > > > > > galaxy.tools ERROR 2011-10-20 13:18:47,722 error reading tool from path: > toolshed/nlstradamus/tools/protein_analysis/nlstradamus.txt > > Traceback (most recent call last): > > File "/home/galaxy/software/galaxy-central/lib/galaxy/tools/__init__.py", > line 106, in load_tool_tag_set > > tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) > > File "/home/galaxy/software/galaxy-central/lib/galaxy/tools/__init__.py", > line 186, in load_tool > > tree = util.parse_xml( config_file ) > > File "/home/galaxy/software/galaxy-central/lib/galaxy/util/__init__.py", > line 105, in parse_xml > > tree = ElementTree.parse(fname) > > File > "/home/galaxy/software/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", > line 859, in parse > > tree.parse(source, parser) > > File > "/home/galaxy/software/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", > line 583, in parse > > parser.feed(data) > > File > "/home/galaxy/software/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", > line 1242, in feed > > self._parser.Parse(data, 0) > > ExpatError: syntax error: line 1, column 0 > That looks like a XML error from something associated with one of my wrappers on the Tool Shed (nlstradamus). Is that something you've installed locally? Was it running fine before updating Galaxy? Do you have any other tools from the Tool Shed and are they working? I haven't yet updated our local install since all the Tool Shed Integration stuff started happening. 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Few possible galaxy bugs ?
On Mon, Oct 24, 2011 at 3:55 PM, michael burrell (TOC) wrote: > Good afternoon Peter, > > Thank you for your rapid response, > > My understanding is that this tool was installed locally from the tool shed, > unfortunately I do not know if it was working before the update was performed. > > Other tools installed from the tool shed do not seem to report errors, would > you have any advice on resolving the small nlstradamus issue that is reported > here? > > Thanks again for the information. > > Michael. I'm hoping Greg can give some clues. This part suggests Galaxy is trying to read the text readme file as if it were XML: galaxy.tools ERROR 2011-10-20 13:18:47,722 error reading tool from path: toolshed/nlstradamus/tools/protein_analysis/nlstradamus.txt ... ExpatError: syntax error: line 1, column 0 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Few possible galaxy bugs ?
Hello Michael, I don't think the ability to automatically install tools from a tool shed into a local Galaxy instance has been made available in the Galaxy distribution yet. Have you updated you Galaxy instance from Galaxy central? What version of Galaxy are you running? Greg Von Kuster On Oct 24, 2011, at 11:02 AM, Peter Cock wrote: > On Mon, Oct 24, 2011 at 3:55 PM, michael burrell (TOC) > wrote: >> Good afternoon Peter, >> >> Thank you for your rapid response, >> >> My understanding is that this tool was installed locally from the tool shed, >> unfortunately I do not know if it was working before the update was >> performed. >> >> Other tools installed from the tool shed do not seem to report errors, would >> you have any advice on resolving the small nlstradamus issue that is >> reported here? >> >> Thanks again for the information. >> >> Michael. > > I'm hoping Greg can give some clues. This part suggests Galaxy is > trying to read the text readme file as if it were XML: > > galaxy.tools ERROR 2011-10-20 13:18:47,722 error reading tool from > path: toolshed/nlstradamus/tools/protein_analysis/nlstradamus.txt > ... > ExpatError: syntax error: line 1, column 0 > > 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: > > http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@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/
