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_...
--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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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