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/source/d/distribute/distribute-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!
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alittleboy
It seems like you do not have connectivity on the box you are trying to install pysam. I will assume you downloaded 'pysam-0.7.4.tar.gz' and are doing something along the lines:
$ pip install pysam-0.7.4.tar.gz
Or:
$ tar xf pysam-0.7.4.tar.gz
$ cd pysam-0.7.4/
$ python setup.py install
In both cases dependencies for pysam will try to be installed automatically. If you cannot configure connectivity in this box(you are behind a firewall or no connectivity at all), you need to satisfy these dependencies manually. As far as I can tell pysam needs distribute and cython.
Thanks! I think it's the problem of firewall... I will try to install them separately to see if it works ;-)
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Are you behind an HTTP proxy? In that case, you will have to set up the http_proxy variable in order for pip to work correctly (http://stackoverflow.com/questions/11726881/how-to-set-an-http-proxy-in-python-2-7)