Branden,

Thank you for reporting this issue, I've committed a fix in 9662:6c462a5a566d. You should be able to re-run your tool migration after updating to that revision.


   --Dave B.

On 5/7/13 11:09:31.000, Branden Timm wrote:
I recently upgraded to the latest galaxy-central, and was advised on
first run that two tools in tool_conf.xml had been removed from the
distribution, but could be installed from the tool shed.  I ran the
script that it generated, however the script fails with the following
messages:

No handlers could be found for logger
"galaxy.tools.parameters.dynamic_options"
/home/GLBRCORG/galaxy/galaxy-central/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
Skipping automatic install of repository ' bowtie_wrappers ' because it
has already been installed in location
../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/0c7e4eadfb3c

Traceback (most recent call last):
   File "./scripts/migrate_tools/migrate_tools.py", line 21, in <module>
     app = MigrateToolsApplication( sys.argv[ 1 ] )
   File
"/home/GLBRCORG/galaxy/galaxy-central/lib/tool_shed/galaxy_install/migrate/common.py",
line 76, in __init__
     install_dependencies=install_dependencies )
   File
"/home/GLBRCORG/galaxy/galaxy-central/lib/tool_shed/galaxy_install/install_manager.py",
line 75, in __init__
     self.install_repository( repository_elem, install_dependencies )
   File
"/home/GLBRCORG/galaxy/galaxy-central/lib/tool_shed/galaxy_install/install_manager.py",
line 319, in install_repository
     install_dependencies=install_dependencies )
   File
"/home/GLBRCORG/galaxy/galaxy-central/lib/tool_shed/galaxy_install/install_manager.py",
line 203, in handle_repository_contents
     persist=True )
   File
"/home/GLBRCORG/galaxy/galaxy-central/lib/tool_shed/util/metadata_util.py",
line 594, in generate_metadata_for_changeset_revision
     tool, valid, error_message = tool_util.load_tool_from_config( app,
app.security.encode_id( repository.id ), full_path )
AttributeError: 'MigrateToolsApplication' object has no attribute
'security'

Any help would be greatly appreciated.  Thanks!

--
Branden Timm
bt...@energy.wisc.edu

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