pip install

[hmontenegro]

bx-python does not install completely with pip install bx-python, as some shared libraries are not compiled:

bbi_file.so, bigbed_file.so, bigwig_file.so, bpt_file.so, cirtree_file.so

This causes problems with other packages, e.g. this issue with CrossMap.

One needs to download from PyPI and install with pip install bx-python-0.7.3.tar.gz

[TyberiusPrime]

Also, for pip to evaluate the requirements, numpy must have been installed previously, preventing install in a clean virtual environment.

[nsoranzo]

Installing from wheels (which are available for recent releases on PyPI) should solve this.