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?
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.
{{{
$ 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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