I just upgrade our galaxy to the latest release : 7487:be81990d148a and
ran the migration tool script for freebayes.
I received the following error:
No handlers could be found for logger "galaxy.tools"
/opt/galaxy/galaxy_dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
RuntimeWarning: __builtin__.file size changed, may indicate binary
incompatibility
from csamtools import *
Repositories will be installed into configured tool_path location
../shed_tools
Adding new row (or updating an existing row) for repository 'freebayes' in
the tool_shed_repository table.
Traceback (most recent call last):
File "./scripts/migrate_tools/migrate_tools.py", line 21, in <module>
app = MigrateToolsApplication( sys.argv[ 1 ] )
File "/opt/galaxy/galaxy_dist/lib/galaxy/tool_shed/migrate/common.py",
line 150, in __init__
install_dependencies=install_dependencies )
File "/opt/galaxy/galaxy_dist/lib/galaxy/tool_shed/install_manager.py",
line 37, in __init__
self.install_repository( repository_elem, install_dependencies )
File "/opt/galaxy/galaxy_dist/lib/galaxy/tool_shed/install_manager.py",
line 262, in install_repository
install_dependencies=install_dependencies )
File "/opt/galaxy/galaxy_dist/lib/galaxy/tool_shed/install_manager.py",
line 150, in handle_repository_contents
repository_tools_tups = get_repository_tools_tups( self.app,
metadata_dict )
File "/opt/galaxy/galaxy_dist/lib/galaxy/util/shed_util.py", line 1077,
in get_repository_tools_tups
tool = app.toolbox.load_tool( os.path.abspath( relative_path ),
guid=guid )
File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 452, in
load_tool
return ToolClass( config_file, root, self.app, guid=guid )
File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 790, in
__init__
self.parse( root, guid=guid )
File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 961, in
parse
self.parse_inputs( root )
File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1045,
in parse_inputs
display, inputs = self.parse_input_page( page, enctypes )
File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1447,
in parse_input_page
inputs = self.parse_input_elem( input_elem, enctypes )
File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1514,
in parse_input_elem
case.inputs = self.parse_input_elem( case_elem, enctypes, context )
File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1470,
in parse_input_elem
group.inputs = self.parse_input_elem( elem, enctypes, context )
File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1540,
in parse_input_elem
param = self.parse_param_elem( elem, enctypes, context )
File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1552,
in parse_param_elem
param = ToolParameter.build( self, input_elem )
File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py", line
176, in build
return parameter_types[param_type]( tool, param )
File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py", line
1361, in __init__
ToolParameter.__init__( self, tool, elem )
File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py", line
43, in __init__
self.validators.append( validation.Validator.from_element( self, elem )
)
File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/validation.py",
line 23, in from_element
return validator_types[type].from_element( param, elem )
File "/opt/galaxy/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 "/opt/galaxy/galaxy_dist/lib/galaxy/tools/data/__init__.py", line
25, in __getitem__
return self.data_tables.__getitem__( key )
KeyError: 'sam_fa_indexes'
What happen is that the freebayes itself installs correctly into
the shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/* but the dependency on
samtools 1.1.8 fails.
The value 'sam_fa_indexes' is present in the tool_data_table_conf.xml and
I know it works since all my samtools are functional.
The status column for the freebayes entry in the database is 'Cloning'.
I get the same error if I try to install freebayes thru the web front end.
( Had to delete the row in the db and remove the freebayes install
directory)
Any ideas Greg?
Thanks!
Philip Mabon (Takadonet)
Senior Bioinformatician
National Microbiology Laboratory
Public Health Agency of Canada
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