Use pip. There is also an install script (Linux only).
Get the latest:
$ pip install https://bitbucket.org/mirnylab/mirnylib/get/tip.tar.gz
Or clone the repo, build extensions, and install in development mode:
$ hg clone https://bitbucket.org/mirnylab/mirnylib $ cd mirnylib $ python setup.py build_ext --inplace $ pip install -e .
For the h5py package to install properly, you need to have the shared library and development headers for HDF5 1.8.4 or newer installed (
libhdf5-dev or similar). See the h5py docs for more information.
- numpy (1.6+)
- joblib (0.6.3+)
- bx-python (preferably from the bitbucket repo by james_taylor)
- Cython (0.16+) to build Cython extensions from .pyx source (C files no longer provided)
We highly recommend using the conda package/environment manager if you have trouble building the core scientific Python packages.
$ conda install numpy scipy matplotlib h5py cython