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Error trying to enable samtools_mpileup
by Waldron, Michael H 01 Mar '12

01 Mar '12

I am running a local copy of Galaxy, last ran 'hg pull -u' on 2/20/12. I am trying to enable use of Mpileup for SAM Tools, and have added the entry for the samtools_mpileup.xml file in tool_conf.xml. However, when I startup Galaxy, the link for Mpileup does not appear in the Tools pane, and I see the following errors from the Galaxy startup: galaxy.tools ERROR 2012-02-29 16:28:51,919 error reading tool from path: samtools/samtools_mpileup.xml Traceback (most recent call last): File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 212, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 305, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 531, in __init__ self.parse( root, guid=guid ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 641, in parse self.parse_inputs( root ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 723, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 922, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 989, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 945, in parse_input_elem group.inputs = self.parse_input_elem( elem, enctypes, context ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 1015, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 1027, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 1330, in __init__ ToolParameter.__init__( self, tool, elem ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/data/__init__.py", line 21, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'sam_fa_indexes' Can someone tell me what is wrong here? Am I missing something in the database? Thanks, Mike Waldron

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Getting errors trying to enable samtools_mpileup
by Jennifer Jackson 01 Mar '12

01 Mar '12

Hello Mike, I am going to move your question over to the galaxy-dev(a)bx.psu.edu mailing list, which is for the discussion of local instance questions. Some things to double check: SAMTools is already set up correctly, with indexes? http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup -> see "SAM Tools installation" If you are still running pile-up, note that two versions of SAMTools are required: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies Including some reorganization to accommodate both versions, as explained in this wiki: http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies Hopefully this helps, Best, Jen Galaxy team On 3/1/12 5:49 AM, Waldron, Michael H wrote: > I am running a local copy of Galaxy, last ran 'hg pull -u' on 2/20/12. > > I am trying to enable use of Mpileup for SAM Tools, and have added the > entry for the samtools_mpileup.xml file in tool_conf.xml. However, when > I startup Galaxy, the link for Mpileup does not appear in the Tools > pane, and I see the following errors from the Galaxy startup: > > galaxy.tools ERROR 2012-02-29 16:28:51,919 error reading tool from path: > samtools/samtools_mpileup.xml > Traceback (most recent call last): > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 212, in load_tool_tag_set > tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 305, in load_tool > return ToolClass( config_file, root, self.app, guid=guid ) > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 531, in __init__ > self.parse( root, guid=guid ) > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 641, in parse > self.parse_inputs( root ) > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 723, in parse_inputs > display, inputs = self.parse_input_page( page, enctypes ) > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 922, in parse_input_page > inputs = self.parse_input_elem( input_elem, enctypes ) > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 989, in parse_input_elem > case.inputs = self.parse_input_elem( case_elem, enctypes, context ) > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 945, in parse_input_elem > group.inputs = self.parse_input_elem( elem, enctypes, context ) > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 1015, in parse_input_elem > param = self.parse_param_elem( elem, enctypes, context ) > File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", > line 1027, in parse_param_elem > param = ToolParameter.build( self, input_elem ) > File > "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", > line 176, in build > return parameter_types[param_type]( tool, param ) > File > "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", > line 1330, in __init__ > ToolParameter.__init__( self, tool, elem ) > File > "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", > line 43, in __init__ > self.validators.append( validation.Validator.from_element( self, elem ) ) > File > "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py", > line 23, in from_element > return validator_types[type].from_element( param, elem ) > File > "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py", > line 279, in from_element > tool_data_table = param.tool.app.tool_data_tables[ table_name ] > File > "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/data/__init__.py", > line 21, in __getitem__ > return self.data_tables.__getitem__( key ) > KeyError: 'sam_fa_indexes' > > Can someone tell me what is wrong here? Am I missing something in the > database? > > Thanks, > > Mike Waldron > > > > ___________________________________________________________ > 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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en/disable field based on the state of checkbox/radiobutton
by Keith Sheppard 01 Mar '12

01 Mar '12

Hello, From looking at the documentation for tool config syntax and I wasn't able to spot a way to have a field enabled or disabled based on the state of a radio button or checkbox. Is this possible? If I missed the documentation please point me in the right direction. I have two use cases for this: the first is that I want the user to be able to either select from a group of preselected values (in my case genome lengths) or enter their own value in a numeric field; the second is that I'd like the user to be able to select from a data file that has been stored on our server or a data file from their history. Thank you, Keith

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March 2012 Galaxy Update
by Dave Clements 29 Feb '12

29 Feb '12

Hello all, The March 2012 Galaxy Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02>is now available. *Galaxy Update <http://wiki.g2.bx.psu.edu/GalaxyUpdates>* is a (mostly) monthly summary of what is going on in the Galaxy community. *Galaxy Updates * complements the *Galaxy Development News Briefs<http://wiki.g2.bx.psu.edu/DevNewsBriefs> * which accompany new Galaxy releases and focus on Galaxy code updates. *Highlights:* - 28 New Papers<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#New_Papers> - Open Positions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#Who.27s_Hiring>at four different institutions - Upcoming Events and Deadlines<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#Upcoming_Events_and_Deadlin…> - GCC2012 Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#GCC2012_Update>, including - Abstract submission is open. - Training Day topics are set. - Tool Shed Contributions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#Tool_Shed_Contributions> If you have anything you would like to see in the April *Galaxy Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates> *, please let me know. Thanks, Dave C. -- http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Problem previewing a tool in the Toolshed
by Carlos Borroto 29 Feb '12

29 Feb '12

Hi, I'm currently developing my first Galaxy tool. I'm working on a wrapper for R's library cummeRbund[1]. I got to the point where the tool although incomplete on functionality, I think is ready to be uploaded to the Toolshed. I was able to do so. I also made sure I could then install it on my local instance using the toolshed repository. Everything is working as expected, except, the tool preview is not working correctly. There is no error, but the inputs, most of them conditional inputs, aren't being displayed correctly. This is the direct link to the tool in the test toolshed: http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?operation=vi… [1]http://compbio.mit.edu/cummeRbund/ Kind regards, Carlos

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mrFAST web interface definition file.
by Luobin Yang 29 Feb '12

29 Feb '12

I noticed that mrFAST is listed in the Galaxy tool shed, but the downloadable files are the source code of mrFAST program itself instead of the web interface XML file. Does mrFAST have a web interface definition file and a possible wrapper program? Thanks, Luobin

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Galaxy-Development site error
by Iry Witham 28 Feb '12

28 Feb '12

Good Morning, I have been attempting to go to the the Galaxy-Dev site this morning at http://gmod.827538.n3.nabble.com/Galaxy-Development-f815885.html and Get a "Content Encoding Error" message. The error says that "The page you are trying to view cannot be shown because it uses an invalid or unsupported form of compression". This happens with Firefox 3.6.27, but not with Crome or Safari. By default I use Firefox 3.6.x due to performance issues with the later versions. Thanks, Iry Witham Scientific Applications Administrator Scientific Computing Group Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.witham(a)jax.org

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Tutorials for SICER
by Vidya .H.K 28 Feb '12

28 Feb '12

Hi, I am exploring SICER peak calling tool for ChIP seq data analysis. Can anyone suggest me tutorial site for galaxy SICER tool?? Regards H.K.VIDYA

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Timeout and Galaxy - Cluster could not complete job
by Aurélien Bernard 28 Feb '12

28 Feb '12

Hello everybody :) Today, I have a question related to timeout management in Galaxy. More particularly, I'm searching for a way to set (in a configuration file if possible) all timeouts related to DRMAA and timeouts related to communication between Galaxy and SGE. My goal is to increase current timeouts to avoid the "Cluster could not complete job" error on successful jobs when there is a temporary problem of "job status checking" (due to heavy write load on the hard drive or whatever). Is this possible ? Thank you in advance, Have a nice day A. Bernard -- Aurélien Bernard IE Bioprogrammeur - CNRS Université des sciences Montpellier II Institut des Sciences de l'Evolution France

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[API] allow_user_impersonation
by Louise-Amélie Schmitt 28 Feb '12

28 Feb '12

Hello everyone! I just wanted to know if the user impersonation will be available through the API someday :) It could be veeery useful for triggering automatic QA on the data without having to share the resulting histories afterwards. Best regards, L-A

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