Hello Shantanu,
Sorry for the delay on this - I've been backed up since the weekend when we
were trading emails. The way Galaxy works with eggs is fairly complex with
regard to handling conflicts, which is undoubtedly what is happening in your
environment since you have the mercurial package installed for your Python 2.6.
Your environment probably results in a conflict that is not properly handled
by the version_conflict() method in ~/lib/galaxy/eggs/__init__.py.
On Jun 4, 2012, at 4:04 PM, Shantanu Pavgi wrote:
>
> Just want to update on the list about this error. I had followed up with Greg
> on this issue off-list as I didn't want to share all the hg output here on
> the list.
>
> The galaxy had downloaded Mercurial egg however it's directory wasn't defined
> in the PYTHONPATH environment variable. However, it was included in the
> sys.path which I verified by printing it in the tool migration application.
> While debugging this issue, I downloaded Mercurial (egg) externally using
> easy_install tool and set up PYTHONPATH to point to this external Mercurial
> egg. After this the tool migration script worked fine.
>
> So should this galaxy-mercurial egg directory and other galaxy egg
> directories be included in the PYTHONPATH environment variable?
For Galaxy, you really don't have to set PYTHONPATH at all, so if you are not
using it for other Python related stuff on your Galaxy server, try unsetting
it, and Galaxy's mercurial egg will probably be found. If you need PYTHONPATH
set, take a look at the version_conflict() method in
~/lib/galaxy/eggs/__init__.py and see if you can figure out what is not being
handled in your environment.
>
> Also, I noticed that tool migration application failed again when I had
> default sqlite database URL mentioned in the universe_wsgi.ini file as it is
> (commented out). It works fine if the default database URL is uncommented.
I'll take a look at this. Thanks for reporting it.
>
> {{{
> $ sh ./scripts/migrate_tools/0002_tools.sh
> Traceback (most recent call last):
> File "./scripts/migrate_tools/migrate_tools.py", line 21, in <module>
> app = MigrateToolsApplication( sys.argv[ 1 ] )
> File
> "/home/shantanu/tmp/galaxy-dist/lib/galaxy/tool_shed/migrate/common.py", line
> 81, in __init__
> object_store=self.object_store )
> File "/home/shantanu/tmp/galaxy-dist/lib/galaxy/model/mapping.py", line
> 1836, in init
> load_egg_for_url( url )
> File "/home/shantanu/tmp/galaxy-dist/lib/galaxy/model/mapping.py", line
> 1816, in load_egg_for_url
> dialect = guess_dialect_for_url( url )
> File "/home/shantanu/tmp/galaxy-dist/lib/galaxy/model/mapping.py", line
> 1812, in guess_dialect_for_url
> return (url.split(':', 1))[0]
> AttributeError: 'bool' object has no attribute 'split'
>
> }}}
>
> --
> Thanks,
> Shantanu
>
> On Jun 1, 2012, at 6:29 PM, Greg Von Kuster wrote:
>
>> Hello Shantanu,
>>
>> What is the result of typing the following in your Galaxy installation
>> directory?
>>
>> hg heads
>>
>> Als, the result of the following:
>>
>> hg status
>>
>> And finally, the results of the following:
>>
>> hg diff
>>
>> Thanks!
>>
>> Greg Von Kuster
>>
>>
>> On Jun 1, 2012, at 5:12 PM, Shantanu Pavgi wrote:
>>
>>>
>>> I am trying to migrate EMBOSS tools from core galaxy code dir to shed_tools
>>> directory. I am getting following error with the migration script:
>>>
>>> {{{
>>> sh ./scripts/migrate_tools/0002_tools.sh
>>> Traceback (most recent call last):
>>> File "./scripts/migrate_tools/migrate_tools.py", line 21, in <module>
>>> app = MigrateToolsApplication( sys.argv[ 1 ] )
>>> File "/home/pavgi/galaxy-exp/lib/galaxy/tool_shed/migrate/common.py", line
>>> 81, in __init__
>>> object_store=self.object_store )
>>> File "/home/pavgi/galaxy-exp/lib/galaxy/model/mapping.py", line 1836, in
>>> init
>>> load_egg_for_url( url )
>>> File "/home/pavgi/galaxy-exp/lib/galaxy/model/mapping.py", line 1816, in
>>> load_egg_for_url
>>> dialect = guess_dialect_for_url( url )
>>> File "/home/pavgi/galaxy-exp/lib/galaxy/model/mapping.py", line 1812, in
>>> guess_dialect_for_url
>>> return (url.split(':', 1))[0]
>>> AttributeError: 'bool' object has no attribute 'split'
>>> }}}
>>>
>>> Following are tool shed related config files:
>>>
>>> {{{
>>> $ cat tool_sheds_conf.xml
>>> <?xml version="1.0"?>
>>> <tool_sheds>
>>> <tool_shed name="Galaxy main tool shed"
>>> url="http://toolshed.g2.bx.psu.edu/"/>
>>> <tool_shed name="Galaxy test tool shed"
>>> url="http://testtoolshed.g2.bx.psu.edu/"/>
>>> </tool_sheds>
>>>
>>>
>>> $ cat shed_tool_conf.xml
>>> <?xml version="1.0"?>
>>> <toolbox tool_path="../shed_tools">
>>> </toolbox>
>>>
>>> }}}
>>>
>>> I am using system Python 2.6 on CentOS 6.2 system. However, I was able to
>>> reproduce this error on CentOS 5.8 system with custom Python 2.6 install as
>>> well. Any pointers on what might be wrong here will be really helpful.
>>>
>>> --
>>> Thanks,
>>> Shantanu
>>>
>>>
>>>
>>>
>>>
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>>
>
>
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