Installation

TCUP is written in Python 3.5 and runs on both Windows and Linux. The installation instructions in this document aim to serve both these platforms, but examples are given in Linux environments. Where notable difference between Windows and Linux install procedure exists, they will be pointed out. This guide assumes the user is reasonably familiar with the command prompt/terminal of these operating systems.

Note

We recommend using Anaconda Python. Anaconda Python runs on Windows and Linux and requires no administrator privileges, and can be installed in your user’s home directory. Download and install Anaconda Python 3.5 (or Miniconda Python 3.5) using the instructions on their website.

If you are unable to use Mercurial (hg) in your environment, you can download a zipfile with the most recent version of TCUP from the Bitbucket repository. If you download TCUP using the zipfile in the above link, just skip any Mercurial (hg) related instructions below.

Install with Anaconda Python

Use Mercurial (hg) to clone the repository available via Bitbucket page to download the source code to be able to install the package:

hg clone https://bitbucket.org/chalmersmathbioinformatics/tcup

This creates a folder tcup in your current directory containing the source code for TCUP. Change into the directory you downloaded (e.g. cd tcup). Now, create a Conda environment into which you will install all dependencies required to run TCUP. The following commands will create a conda environment named “tcup”, containing all the required dependencies, into which you will also install TCUP itself. Replace <platform> with the platform you are installing TCUP on (Linux or Windows):

conda env create -f conda_environment_<platform>.yml

After creating the conda environment, activate the environment and install TCUP into it (Windows users activate by typing activate tcup, omitting source):

source activate tcup
cd tcup
pip install .

Now you can read the section Running TCUP for information on how to use TCUP, or have a look at the Tutorial for a more brief introduction.

Download source code for TCUP

The complete source code for TCUP can be downloaded from the project’s Bitbucket page, either by downloading a zipfile of the most recent version from the webpage, or using Mercurial (hg):

hg clone https://bitbucket.org/chalmersmathbioinformatics/tcup

This is useful if you want to help improve TCUP. Consult the CONTRIBUTING file in the project root folder for information on how to contribute to TCUP.