Error installing migrated tool deps

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Error installing migrated tool deps

Branden Timm-2
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
[hidden email]

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Re: Error installing migrated tool deps

Dave Bouvier
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
> [hidden email]
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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Re: Error installing migrated tool deps

Branden Timm-2
Confirmed working, thanks!

-Branden

On 5/7/2013 1:25 PM, Dave Bouvier wrote:

> 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
>> [hidden email]
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/