Question: Getting Errors Trying To Enable Samtools_Mpileup
0
gravatar for Waldron, Michael H
6.2 years ago by
Waldron, Michael H10 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
mpileup samtools bam • 908 views
ADD COMMENTlink modified 6.2 years ago by Jennifer Hillman Jackson24k • written 6.2 years ago by Waldron, Michael H10
0
gravatar for Jennifer Hillman Jackson
6.2 years ago by
United States
Jennifer Hillman Jackson24k wrote:
Hello Mike, I am going to move your question over to the galaxy-dev@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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
ADD COMMENTlink written 6.2 years ago by Jennifer Hillman Jackson24k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 129 users visited in the last hour