Pysam installation problem in Red Hat Linux

[alittleboy]

When installing the pysam Python module, version 0.7.4, it seems that the setup.py code first downloads "distribute" as below:

Downloading http://pypi.python.org/packages/sour...-0.6.34.tar.gz

On the server, it took a long time to respond with an error: connection timeout. Is there a way to get rid of this step? If there is another way of installing Pysam that would be great. Thanks!

[GenoMax]

Your local institutional firewall may be blocking access to the python.org site.

Pysam is available here: http://code.google.com/p/pysam/downloads/list

[lac302]

Does this look like a proxy issue? Results from: $ python setup.py build

[root@g300-149-b0 pysam-0.7.4]# python setup.py build
Downloading http://pypi.python.org/packages/sour...-0.6.34.tar.gz
Traceback (most recent call last):
File "setup.py", line 127, in <module>
use_setuptools()
File "/app/pysam-0.7.4/distribute_setup.py", line 169, in use_setuptools
download_delay)
File "/app/pysam-0.7.4/distribute_setup.py", line 131, in _do_download
to_dir, download_delay)
File "/app/pysam-0.7.4/distribute_setup.py", line 201, in download_setuptools
src = urlopen(url)
File "/usr/lib64/python2.6/urllib2.py", line 126, in urlopen
return _opener.open(url, data, timeout)
File "/usr/lib64/python2.6/urllib2.py", line 397, in open
response = meth(req, response)
File "/usr/lib64/python2.6/urllib2.py", line 510, in http_response
'http', request, response, code, msg, hdrs)
File "/usr/lib64/python2.6/urllib2.py", line 429, in error
result = self._call_chain(*args)
File "/usr/lib64/python2.6/urllib2.py", line 369, in _call_chain
result = func(*args)
File "/usr/lib64/python2.6/urllib2.py", line 616, in http_error_302
return self.parent.open(new, timeout=req.timeout)
File "/usr/lib64/python2.6/urllib2.py", line 391, in open
response = self._open(req, data)
File "/usr/lib64/python2.6/urllib2.py", line 409, in _open
'_open', req)
File "/usr/lib64/python2.6/urllib2.py", line 369, in _call_chain
result = func(*args)
File "/usr/lib64/python2.6/urllib2.py", line 1198, in https_open
return self.do_open(httplib.HTTPSConnection, req)
File "/usr/lib64/python2.6/urllib2.py", line 1165, in do_open
raise URLError(err)
urllib2.URLError: <urlopen error [Errno -2] Name or service not known>

[A.N.Other]

Quite possible.

If you are behind a proxy server, are you configured to go through it? What's the contents of your /etc/environment ?

You can add the following lines to it ... obviously customising as appropriate:

no_proxy=localhost,127.0.0.0/8,*.local
NO_PROXY=localhost,127.0.0.0/8,*.local
all_proxy=socks://proxy.example.com:8080/
ALL_PROXY=socks://proxy.example.com:8080/
http_proxy=http://proxy.example.com:8080
HTTP_PROXY=http://proxy.example.com:8080
ftp_proxy=http://proxy.example.com:8080
FTP_PROXY=http://proxy.example.com:8080
https_proxy=http://proxy.example.com:8080
HTTPS_PROXY=http://proxy.example.com:8080

[lac302]

It turns out I needed to have my hostname identified in /etc/hosts file for python to work with urlopen