Installation

Quick start

The TOBIAS package is available on PyPI to install via:

$ pip install tobias

or as a Conda package on the Bioconda channel:

$ conda install tobias -c bioconda

The TOBIAS tools will then be available from the commandline:

$ TOBIAS (...)

Description of each tool is found by running TOBIAS 'TOOLNAME' --help or in the Tool overview.

Dependencies

For some tools, external programs such as 'samtools' and 'bedtools' are needed. For 'TOBIAS MotifClust', the python package 'gimmemotifs' is needed. We therefore recommend using the included conda environment to install dependencies of TOBIAS:

$ git clone https://github.com/loosolab/TOBIAS.git
$ cd TOBIAS
$ conda env create -f tobias_env.yaml
$ source activate TOBIAS_ENV

Next, you can install TOBIAS into the environment as explained above.

Install from GitHub

To install directly from the repository, the python package Cython is needed to build the C-extensions used by TOBIAS. You can obtain Cython with pip install cython. TOBIAS can then be installed using the setup.py script:

$ git clone https://github.com/loosolab/TOBIAS.git
$ cd TOBIAS
$ python setup.py install