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Some eggs are out of date, attempting to fetch...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

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