Hi Xiaofei, It is best to keep replied on the mailing list. First, confirm that you are running the most current version of the Galaxy distribution. This should be true by default if the installation was just performed. https://wiki.galaxyproject.org/DevNewsBriefs https://wiki.galaxyproject.org/DevNewsBriefs/2014_02_10 Since you ran into this issue the first time the server was brought up (or this appears to be the case), you may have run into a characterized issue. On the http://getgalaxy.org page, are two work-arounds for installing eggs in under specific usage circumstances. One is for when running without internet access (probably not the issue). The other is for when using Python 2.7 (my best guess as the problem). Both are included about half-way down the wiki page, toward the end of the 'Start it up' section: https://wiki.galaxyproject.org/Admin/GetGalaxy Please review and see if either if these apply, in particular if the second command ("sh run.sh --reload") solves the issue. Again, please keep feedback on the list, so that the developers can assist us going forward as needed, Jen Galaxy team On 2/24/14 9:51 AM, Wang, Xiaofei wrote:

Dear Jen,

I really appreciate for your reply!

We decided to install the local Galaxy for this project. But, when I installed it (I followed the instruction on these 2 links, http://gmod.org/wiki/Galaxy_Tutorial_2013 and https://wiki.galaxyproject.org/Admin/GetGalaxy), I got a problem like this:

$ sh run.sh Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 37, in <module> c.resolve() # Only fetch eggs required by the config File "/Volumes/saturn/xiaofei/software/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Volumes/saturn/xiaofei/software/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Volumes/saturn/xiaofei/software/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pkg_resources.py", line 576, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: pysam==0.4.2-kanwei-b10f6e722e9a Fetch failed.

It seems a problem with the Python '"eggs". But, when I checked the version of Python, it is: $ python --version Python 2.7.6

Could you help me about what is the problem with the installation?

Thank you so much!

Best,

Xiaofei