On Mar 13, 2012, at 11:08 AM, Alban Lermine wrote:
Hi Alban,
Is your Galaxy server behind a firewall or without network access such that it cannot access http://eggs.g2.bx.psu.edu/ ?
What happens if you run `python scripts/fetch_eggs.py` by hand?
Is there a way to downgrade Galaxy?
Yes, in most cases you can downgrade with `hg update -r <old changeset id>`.
--nate
Thanks by advance for your answer..
Alban
-- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84
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Re,
Thanks for your fast answer..
I run fetch_eggs.py by hand, here is the return:
Fetched http://eggs.g2.bx.psu.edu/boto/boto-2.2.2-py2.6.egg Removed conflicting egg: <galaxy_dir>/galaxy-dist/eggs/boto-1.8d-py2.6.egg
I tried then to start Galaxy, and I also have a new error message:
Traceback (most recent call last): File "/bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/app.py", line 24, in __init__ self.config.check() File "/bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/config.py", line 254, in check raise ConfigurationError( "Unable to create missing directory: %s\n%s" % ( path, e ) ) ConfigurationError: Unable to create missing directory: ./../shed_tools [Errno 13] Permission denied: './../shed_tools'
It seems it's now only a permission problem.. (I only have rights on galaxy-dist directory), I will ask our system engineer to rerun update..
Hi Alban, You can fix this one by changing the path to the shed_tools directory in shed_tool_conf.xml. It can be any directory you can write to, but should not be underneath the galaxy-dist directory. --nate
Alban
-- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84