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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