Re: [galaxy-user] Weblogo results empty
Hi Ross, thanks for taking care of this issue. On 07/05/2011 12:31 AM, Ross wrote: Is this error seen on Galaxy main or test? If so please share the history with me so I can see the input and reproduce what sounds like a wrapper error? Otherwise, if this is on a private instance, and if the tool has never produced output successfully, then this may be a dependency installation problem - eg you may need to ensure that the weblogo3 executable is available and working correctly on the path used by your execution nodes. To assure yourself that your data works with the tool, please try running it on main using the same data, and let me know what you see? in fact it's a private instance of galaxy, it's the latest version of galaxy-dist (hg summary: 5743:720455407d1c). The input data is fine, it's a clustalw alignment in fasta format which can be used by the weblogo module on galaxy main. Maybe some background info on the weblogo installation helps: it's located below the tool_dependency_dir as defined in universe_wsgi.ini in weblogo/3.0 (with default as a link to 3.0). It contains the file env.sh which sets the PATH: export PATH=/home/galaxy/dependencies/weblogo/3.0:$PATH Starting the weblogo executable with the galaxy virtualenv python seems to work (just tested --help), although it returns a warning: ~/python/bin/python ./weblogo --help/home/galaxy/python/lib/python2.6/site-packages/CoreBio-0.5.0-py2.6.egg/corebio/seq_io/_nexus/__init__.py:19: DeprecationWarning: the sets module is deprecated import sets I also tested putting a link to the weblogo executable in the PATH that's defined for the galaxy user (as opposed to the dependency dir mechanism, that I have to admit I don't fully understand yet), but that also doesn't work. Could this be an issue of PYTHONPATH needing to be adjusted? Regards, Holger Thanks again. On Tue, Jul 5, 2011 at 12:34 AM, Holger Klein h.kl...@imb-mainz.de wrote: Dear all, I have a problem with the weblogo tool. I have a clustalw alignment in fasta format that I'd like to visualize as a logo. The sequence logo module ends with a success (green box), the info tells me the amount and length of the input data. But the output is empty, there are no plots (no matter if I select jpg, png, pdf or text). The respective image can't be displayed because it contains errors or is empty in case of text. I suspect that the actual call of the weblogo tool doesn't succeed, but I didn't figure out yet on how to check this. Does anybody have hints on where to look? Cheers, Holger -- Dr. Holger Klein Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de/ Tel: +49(6131) 39 21511 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Dr. Holger Klein Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de/ Tel: +49(6131) 39 21511 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Several errors from run.sh
Hi all, I am upgrading to the most recent galaxy-dist 720455407d1chttps://bitbucket.org/galaxy/galaxy-dist/changeset/720455407d1c . First time run.sh shows following errors as in attachment. It seems when I use 'manage_db.sh upgrade' it doesn't create necessary tables for these tools. Wonder if these are known issues? Thanks [epigraph] galaxy.tools ERROR 2011-07-05 10:34:12,556 error reading tool from path: data_destination/epigraph.xml Traceback (most recent call last): File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 169, in load_tool return ToolClass( config_file, root, self.app ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 340, in __init__ self.parse( root ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 385, in parse self.interpreter = command.get(interpreter, None) AttributeError: 'NoneType' object has no attribute 'get' galaxy.tools ERROR 2011-07-05 10:34:12,559 error reading tool from path: data_destination/epigraph_test.xml Traceback (most recent call last): File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 169, in load_tool return ToolClass( config_file, root, self.app ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 340, in __init__ self.parse( root ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 385, in parse self.interpreter = command.get(interpreter, None) AttributeError: 'NoneType' object has no attribute 'get' [manipulation] galaxy.tools WARNING 2011-07-05 10:34:16,151 A when tag has been defined for 'manipulation (manipulation_selector) -- modify_each_score', but does not appear to be selectable. [picard] galaxy.tools ERROR 2011-07-05 10:34:16,700 error reading tool from path: picard/picard_ReorderSam.xml Traceback (most recent call last): File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 169, in load_tool return ToolClass( config_file, root, self.app ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 340, in __init__ self.parse( root ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 441, in parse self.parse_inputs( root ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 523, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 703, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 770, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 796, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 808, in parse_param_elem param = ToolParameter.build( self, input_elem ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py, line 161, in build return parameter_types[param_type]( tool, param ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py, line 607, in __init__ self.options = dynamic_options.DynamicOptions( options, self ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py, line 411, in __init__ Data table named '%s' is required by tool but not configured % tool_data_table_name AssertionError: Data table named 'picard_indexes' is required by tool but not configured [mosaik] galaxy.tools ERROR 2011-07-05 10:34:17,217 error reading tool from path: sr_mapping/mosaik.xml Traceback (most recent call last): File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 169, in load_tool return ToolClass( config_file, root, self.app ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 340, in __init__ self.parse( root ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 441, in parse self.parse_inputs( root ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 523, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 703, in parse_input_page inputs = self.parse_input_elem( input_elem,
[galaxy-user] How to re-use a parameter in a workflow?
Galaxy Users, I have a workflow where I'd like the user to input a value once, say a number of nucleotides. That value would then be used as an input parameter to several different tasks, for example, to two instances of Operate on Genomic Intervals Get flanks , where it would be used both for the offset and length of flanking regions(s) in one instance, and it's value and it's *negative* would be used for the second instance. Thus, the user inputs 20, and Get_flanks(20,20) and Get_flanks(-20,20) get run. For this workflow, it's important that those parameters all be of the same magnitude, or things will get messy later, so I don't want the user having to input them separately, or to have to remember which one gets negated... All suggestions welcome, Curtis ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] wiggle file
Hi, this should be simple but it is not..forgive the newbie question. i am doing chip-seq. bowtiesam filter for mapped readsMACS. i want to create a wiggle file that displays in ucsc, but when i choose the WIG option on macs, and then try to show it in UCSC, it treats each line of the created WIG file as a separate track, and obviously does not show it as a graph. is there a wiki page somewhere that can give me the basics? or can someone point me in the right direction? thanks. rich___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
