Pysam Installation Problem In Red Hat Linux
1
0
Entering edit mode
11.1 years ago
alittleboy ▴ 220

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!

• 6.6k views
ADD COMMENT
1
Entering edit mode

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)

ADD REPLY
4
Entering edit mode
11.1 years ago
Carlos Borroto ★ 2.1k

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.

ADD COMMENT
0
Entering edit mode

Thanks! I think it's the problem of firewall... I will try to install them separately to see if it works ;-)

ADD REPLY

Login before adding your answer.

Traffic: 2923 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6