Adding BioNetGen to Anaconda environment

Question

I am trying to use PySB with Anaconda3 and Windows7. I have added the relevant depedencies (numpy, scipy, sympi, perl) to a working environment. However I am struggling with the BioNetGen program. I have downloaded it, and added the path to BNG, but I cannot add it to my environment.

Here is what I have tried:

>conda search bionetgen

Using Anaconda Cloud api site http....
Fetching package metadata...

Then nothing happens.

>pip install bionetgen
Collecting bionetgen

Then error message:

Could not find a version that satisfies the requirement bionetgen (from versions: )
No matching distribution found for bionetgen

Finally, I tried:

>easy_install bionetgen
Processing bionetgen...
error: could not find a setup script in C:\....

However I can open the BioNetGen programme manually and get the gui so I assume it has installed correctly. I just don't know how to add it to anaconda. Is the problem that BioNetGen runs on perl?

There is a Virtual Box available for visualisation the pysb models but I would prefer to install dependencies manually.

Thanks for any help!

Answer 1

Yes, BioNetGen itself is written in Perl and thus can't be installed via pip or other Python package managers. You need to download the BioNetGen command-line interface for your platform and then follow the instructions in the PySB installation documentation to install it where PySB can find it:

Rename the unzipped BioNetGen-x.y.z folder to just BioNetGen and move it into /usr/local/share (Mac or Linux) or C:\Program Files (Windows). If you would like to put it somewhere else, set the BNGPATH environment variable to the full path to the BioNetGen-x.y.z folder.

You mention the BioNetGen "GUI" which leads me to believe you've downloaded the RuleBender GUI interface rather than the command-line tools. The PySB docs don't explicitly state that you need the command-line tools -- we will definitely rectify this oversight.