Dear Galaxians,I am behind a proxy with authentication, and I think I will contribute a wiki page on how to install and configure galaxy for saving other people's time...
In this mail however I would like to propose a change in the
lib/tool_shed/util/common_util.py
The problem I had was that not all tool "wrappers" could be installed using the web interface since I was always getting an error "host not found" generated by the urllib2.py call
From that error message (found in paster.log) it was clear that the problem was due to the fact I am behind a firewall with authentication, and the http_proxy variable in the run.sh was not sufficient.
I then modified lib/tool_shed/util/common_util.py following the instructions that I have found in
and then now finally it works.
Hereafter is what I've modified and it is certainly NOT the appropriate way of doing it from a proper IT point of view (since is not good practice to encode passwords in a source code). Furthermore, with the next mercurial update my code changes will disappear ... I really hope that therefore someone of your smart people could modify the codebase accordingly, perhaps reusing the http_proxy ... proxy_user and proxy_password system variables :-?
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def tool_shed_get( app, tool_shed_url, uri ):
"""Make contact with the tool shed via the uri provided."""
registry = app.tool_shed_registry
#CHANGES FOR PROXY AUTH
password_mgr = urllib2.HTTPPasswordMgrWithDefaultRealm()
proxy_handler=urllib2.ProxyHandler({'http': 'http://myproxy.domain.com:8080'})
proxy_auth_handler=urllib2.ProxyBasicAuthHandler(password_mgr)
urlopener = urllib2.build_opener(proxy_handler,proxy_auth_handler)
# urlopener = urllib2.build_opener()
# password_mgr = registry.password_manager_for_url( tool_shed_url )
# if password_mgr is not None:
# auth_handler = urllib2.HTTPBasicAuthHandler( password_mgr )
# urlopener.add_handler( auth_handler )
response = urlopener.open( uri )
content = response.read()
response.close()
return content