Hi Nate Thanks for your help. The issue was resolved I put detail here for reference to others.
My RHEL username was not the owner of the folder where I was directed to install the software i.e. /opt/. As I am super user so I was running all commands using sudo. This method worked for Mercurial however I did not realize that running galaxy as sudo sh run.sh could read env from root. So I made myself the full owner of the folder and ran galaxy by issuing simple sh run.sh problem solved. Thanks. Regards, Matloob -----Original Message----- From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: Friday, 30 September 2011 5:39 AM To: Matloob Khushi Cc: email@example.com Subject: Re: [galaxy-dev] Setting http_proxy for Python Hi Matloob, It looks like urllib, which Galaxy uses to fetch eggs, can't use authenticated proxies. urllib2 would do it: http://stackoverflow.com/questions/34079/how-to-specify-an-authenticated -proxy-for-a-python-http-connection But this would require some changes to the egg handling code. In the meantime, you could use the egg packaging scripts on a system with an internet connection to fetch the eggs for you. See the instructions at: http://wiki.g2.bx.psu.edu/Admin/Config/Eggs Under "If your Galaxy server does not have Internet access" --nate Matloob Khushi wrote: > Hi Guys > > I am trying to install Galaxy on Red Hat Enterprise Linux Server release > 5.7 (Tikanga). I have installed Python 2.6. Our server is behind a > proxy that needs to be authenticated. I have set up the proxy for > Mercurial as described in > http://www.selenic.com/mercurial/hgrc.5#http-proxy > > > > Now Mercurial is working and I have cloned the repository, however, when > I issue sh run.sh command I get the following error. Though I have set > the environment variable http_proxy by issuing export command on command > line: > > > > export HTTP_PROXY=UserName:myunip...@servername.edu.au:8080 > > I have also tried various export syntax such as: > > export http_proxy=http://UserName:MyUniPass@ servername.edu.au:8080 > > > > I suspect Python is not reading the proxy setting to access internet. > Help please. > > > > Some eggs are out of date, attempting to fetch... > > Traceback (most recent call last): > > File "./scripts/fetch_eggs.py", line 30, in ? > > c.resolve() # Only fetch eggs required by the config > > File "/opt/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in > resolve > > egg.resolve() > > File "/opt/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in > resolve > > return self.version_conflict( e.args, e.args ) > > File "/opt/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in > version_conf lict > > r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), > env, egg. fetch ) > > File "/opt/galaxy-dist/lib/pkg_resources.py", line 565, in resolve > > raise DistributionNotFound(req) # XXX put more info here > > pkg_resources.DistributionNotFound: simplejson==2.1.1 > > Fetch failed. > > > > Regards > > Matloob > > ___________________________________________________________ > 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/