Question: Very strange errors setting up Galaxy local host on a mac
1
gravatar for abe.pressman
4.1 years ago by
abe.pressman20
United States
abe.pressman20 wrote:

I've been trying to set up a local galaxy server on my mac to try things out, but am getting a large pile of weird errors that searches aren't turning up much help for. Python is 2.7.5, Mac OS is 10.9.4.

Specifically, "sh run.sh" always crashes, but has given me different sets of errors. My current set, after several failed runs, starts out:

 

Some eggs are out of date, attempting to fetch...

Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg

One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution.

Dependency "bioblend" requires "nose"

 

This is followed by about 200 lines of DEBUG messages, and then
 

 

galaxy.eggs DEBUG 2014-10-13 19:05:09,654 Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg

galaxy.eggs ERROR 2014-10-13 19:05:09,668 One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution.

galaxy.eggs ERROR 2014-10-13 19:05:09,668 Dependency "bioblend" requires "nose"


...followed by a lot of trackbacks, and then it exits. Anybody know if I'm supposed to try reinstalling, or what?

Thanks!

software error • 878 views
ADD COMMENTlink modified 4.1 years ago by Dannon Baker3.7k • written 4.1 years ago by abe.pressman20

Got an answer. Thanks!

ADD REPLYlink written 4.1 years ago by abe.pressman20
2
gravatar for Dannon Baker
4.1 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

Many of these sorts of issues come from having an 'unclean' environment in which to run galaxy.  See https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_a_clean_environment for more, but basically you should be able to install virtualenv to isolate any external python packages from your Galaxy install.  Once that's done, and you've activated the virtualenv, remove the eggs folder from galaxy (rm -rf <galaxy_folder>/eggs) and start things up again.

Let me know if you have any issues with setting up a virtualenv and I'll try to help!

ADD COMMENTlink written 4.1 years ago by Dannon Baker3.7k
1

Looks like removing eggs fixed it—I just wasn't sure if I could do that safely, but I tried it as you mentioned and it reinstalled them just fine. Thanks!

ADD REPLYlink written 4.1 years ago by abe.pressman20

Great, glad you're up and running!

ADD REPLYlink written 4.1 years ago by Dannon Baker3.7k
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