Installation

Stable release

For a full installation of phenotrex, run this command in your terminal:

$ pip install phenotrex[fasta]

Note that this command installs large dependencies (pytorch, deepnog) required for transforming FASTA files into phenotrex input features at runtime.

If this capability is not needed (for example because feature files have been pre-created), installation size can be significantly reduced by running instead:

$ pip install phenotrex

If you don’t have pip installed, this Python installation guide can guide you through the process.

From sources

The sources for phenotrex can be downloaded from the Github repo.

You can either clone the public repository:

$ git clone git://github.com/univieCUBE/phenotrex

Or download the tarball:

$ curl -OL https://github.com/univieCUBE/phenotrex/tarball/master

Once you have a copy of the source, you can install it with:

$ make full-install