Installation

taco is installed using setup.py, and will be installed as a command-line utility on the system. When we are finished you will be able to run the command

$ taco --help

and see a taco help message.

Requirements

taco requires the following software be installed:

• Python 3
• Conda
• Snakemake
• Singularity or Docker

To check that you are using Python 3, run:

$ /usr/bin/env python --version

To test that Snakemake can be imported from Python, run:

$ /usr/bin/env python -c 'import snakemake'

To check your version of singularity, run:

$ which singularity

Scripts to install the above packages can be found in the scripts/ directory of dahak-taco.

Clone

Start by cloning a local copy of the repository:

git clone https://github.com/dahak-metagenomics/dahak-taco

You can specify a particular tag or branch with the clone command, or use the default stable branch.

Build and Install

The next step is to build and install the taco source code using setup.py:

$ python setup.py build

If you want to install taco as a system level module, run:

$ python setup.py install

If you want to install it as a user (recommended):

$ python setup.py install --user

$ python setup.py install --user --prefix=    # <-- this is required on mac

This will install the taco command line utility as an executable program in the Python bin location. This location may or may not be on your path, and varies depending on your Python environment, but should be in

$PYTHONHOME/bin

This should be on your $PATH for you to be able to call taco from the command line.

Run Tests

To run tests:

python setup.py test