Read the documentation.
The easiest way is to use pip.
First, install mirnylib, e.g:
$ pip install https://bitbucket.org/mirnylab/mirnylib/get/tip.tar.gz
Then install hiclib:
$ pip install https://bitbucket.org/mirnylab/hiclib/get/tip.tar.gz
Or clone the repo and install from there. Alternatively, there is a install script that doesn't use pip (Linux only).
Getting the basic Scientific Python stack can be trickier on some platforms than others. For more details, see the instructions on scipy.org. You should already have these dependencies installed and running correctly before attempting to install this package.
- numpy (1.6+)
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 ...
- Sphinx (to generate documentation)
Mirnylib provides a HDF5 dictionary type based on the Python h5py package. 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-devor similar). See the h5py docs for more information.
You will also need the
bowtie2mapping software which can be downloaded manually or installed via the download_bowtie.sh script in the hiclib folder.