Alicia;
*I hope this is the correct email to contact re. Galaxy cloud. I tried to run Galaxy on the cloud, I could upload the file but could not go beyond simple function "operate on genomic intervals". Is this normal? This is my first time using the Galaxy on the cloud. Hope to hear from you soon. Thank you. *
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/mnt/galaxyTools/galaxy-central/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/local/lib/python2.6/dist-packages/MarkupSafe-0.11-py2.6-linux-x86_64.egg/markupsafe/__init__.pyc, but /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg is being added to sys.path
What method did you use to start up the Galaxy cloud instance? I've seen this problem with recent versions of Galaxy and BioCloudCentral, using the current CloudBioLinux AMI (ami-46d4792f). We have a new version of CloudBioLinux/CloudMan in development which fixes this. In the short term, you could try the Galaxy Cloud Launch page to create your instance:
https://main.g2.bx.psu.edu/cloudlaunch
Dannon and Enis, we could isolate Galaxy inside a virtualenv as a more general fix to these egg conflicts.
Hope this helps, Brad