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

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