Installation¶

Required packages in python: numpy, matplotlib, pysam

• we suggest using Anaconda distribute, which includes most packages (except pysam here), and provides you a user specific environment, i.e., all your python packages go to a single folder. Thus, you don’t need the root to install packages.
• you could install pysam by pypi in terminal, or download and install as diceseq.

You can install DICEseq simply via pypi in terminal (suggested), or upgrade by add --upgrade as follows:

pip install diceseq

pip install --upgrade --no-deps diceseq

Alternatively, you also could download the source code via GitHub (latest version, suggested) or Sourceforge (any version) and run python setup in terminal:

• GitHub: https://github.com/huangyh09/diceseq
• Sourceforge: http://sourceforge.net/projects/diceseq/

python setup.py install

In any case, if had the permission error for installation as you are not root, add --user.