Setting http_proxy for Python
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:MyUniPass@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 Some eggs are out of date, attempting to fetch...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[0], e.args[1] ) 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
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-pro... 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:MyUniPass@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[0], e.args[1] )
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
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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:nate@bx.psu.edu] Sent: Friday, 30 September 2011 5:39 AM To: Matloob Khushi Cc: galaxy-dev@lists.bx.psu.edu 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:MyUniPass@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[0], e.args[1] )
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
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participants (2)
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Matloob Khushi -
Nate Coraor