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 http://stackoverflow.com/questions/34079/how-to-specify-an-authenticated-proxy-for-a-python-http-connection 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 :-? ------------------------------------------------------------------------------------------------------------------ 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() password_mgr.add_password(None, 'http://myproxy.domain.com:8080','MYDOMAIN\MYUSER' , 'MYPASS') 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) #PREVIOUS CODE # 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
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