On Mar 3, 2013, at 5:21 PM, Anusha Nagari wrote:

> Hi,
> 
> I am a new user of galaxy and am trying to set up local version of galaxy on 
> my mac. I followed the instructions in this link and successfully installed 
> the local version using the following steps:
> 
> mkdir galaxy-python/
> mkdir galaxy-dist/
> ln -s /usr/local/bin/ galaxy-python/python
> export PATH=~/galaxy-python:$PATH
> hg clone https://bitbucket.org/galaxy/galaxy-dist/
> cd galaxy-dist
> sh run.sh
> 
> I could load galaxy fine for the first time. However after I closed it and 
> tried to run it by sh run.sh, it is giving the following error and am unable 
> to startup galaxy:
> __import__( "pkg_resources" ).declare_namespace( __name__ )
> Traceback (most recent call last):
> File "./scripts/manage_tools.py", line 12, in <module>
> from migrate.versioning.shell import main
> ImportError: No module named migrate.versioning.shell

Hi Anusha,

I've moved this thread over to the galaxy-dev list since it concerns a local 
installation. Could you check to see if you've set the PYTHONPATH environment 
variable?  It seems that something odd is going on with your environment.  
Also, if you opened a new shell for the second time you executed run.sh, you'll 
need to set the same PATH variable as you did the first time.  That export does 
not persist unless you place it in one of your shell's startup files.

The symlink method is quick and easy, but if you are going to have a persistent 
Galaxy server that you'll be installing python modules in to, I would suggest 
using a virtualenv as described here:

http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_a_clean_environment

--nate

> 
> However, I am not able to upload any datasets into galaxy either from UCSC 
> genome browser or from my computer with the following error:
> An error occurred with this dataset: 
> /Users/anushanagari/Desktop/Softwares/galaxy-dist/lib/galaxy/__init__.py:5: 
> UserWarning: Module site was already imported from 
> /Library/Frameworks/Python.framework/Versions/4.2.30201/lib/python2.5/site.pyc,
>  but /Library/Frameworks/Python.framework/Version
> 
> Tool execution generated the following error message:
> /Users/anushanagari/Desktop/Softwares/galaxy-dist/lib/galaxy/__init__.py:5: 
> UserWarning: Module site was already imported from 
> /Library/Frameworks/Python.framework/Versions/4.2.30201/lib/python2.5/site.pyc,
>  but 
> /Library/Frameworks/Python.framework/Versions/4.2.30201/lib/python2.5/site-packages/Enstaller-3.0.9-py2.5.egg
>  is being added to sys.path
>   __import__( "pkg_resources" ).declare_namespace( __name__ )
> /Users/anushanagari/Desktop/Softwares/galaxy-dist/lib/galaxy/__init__.py:5: 
> UserWarning: Module pkg_resources was already imported from 
> /Users/anushanagari/Desktop/Softwares/galaxy-dist/lib/pkg_resources.pyc, but 
> /Library/Frameworks/Python.framework/Versions/4.2.30201/lib/python2.5/site-packages/Enstaller-3.0.9-py2.5.egg
>  is being added to sys.path
>   __import__( "pkg_resources" ).declare_namespace( __name__ )
> 
> 
> Could you please help me with this and also provide any additional 
> documentation that could help me in getting to know galaxy better? Thanks in 
> advance! Hoping to hear from you soon!
> 
> Best,
> Anusha
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