Thank Nate for your help.
Visualization menu is now effective.
However, I still have the problem of updating eggs. Indeed, galaxy is installed on a virtual machine and jobs run on SGE cluster. But I have been discouraged by my system administrator to run fetch_eggs.py scripts from our cluster node.
If I run `python ./scripts/fetch_eggs.py` in galaxy-dist directory, as Galaxy 
user, but on my virtual machine, missing eggs are not grabed.
Do you have another solution?

Thanks,
Sarah





Nate Coraor a écrit :
On Apr 27, 2012, at 6:00 AM, Sarah Maman wrote:

Hello,


After pulling latest changes (March 2012 - r 40f1816d6857), jobs launched run 
properly (output files OK) but I get the following warning:

/WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be 
fetched/

Hi Sarah,

I'm guessing that you are using a cluster with Galaxy.  If this is correct, 
please try the following:

1. Log in to a cluster node as the user that runs Galaxy
2. cd to the galaxy-dist directory
3. run `python ./scripts/fetch_eggs.py`

This should grab any missing eggs.

In addition, Galaxy GUI is not exactly GUI seen in the cloud 
(https://main.g2.bx.psu.edu/). For example, "Visualization" menu is absent and 
I think it should be related to the previous warning?

See the 'enable_tracks' setting in universe_wsgi.ini to enable the 
Visualization menu.

--nate

How to ensure that eggs be properly fetched?


Thank you in advance,
Sarah Maman
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/

Reply via email to