Read the documentation.
The easiest way is to use pip, but see notes below:
First, install mirnylib:
$ 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
Alternatively, there is a linux install script that doesn't use pip.
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.
Getting the basic Scientific Python stack (numpy/scipy/matplotlib) 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+)
Installed by setuptools if missing:
- Sphinx (to generate documentation)