Installation

Conda

The easiest way to install pharokka is via conda. For inexperienced command line users, this method is highly recommended.

conda install -c bioconda pharokka

This will install all the dependencies along with pharokka. The dependencies are listed in environment.yml.

If you have a MacOS system with M1/M2/M3 Apple Silicon, try this 

conda create --platform osx-64 --name pharokkaENV -c bioconda pharokka
conda activate pharokkaENV

Pip

As of v1.4.0, you can also install the python components of pharokka with pip.

pip install pharokka

You will still need to install the non-python dependencies manually.

Container

If you have Docker/Singularity/Apptainer installed, you can use the biocontainers container (yes, every bioconda package has one!)

You might find this useful if you have trouble with conda environments.

For example to install pharokka v1.7.3 with Singularity:

IMAGE_DIR="<the directory you want the .sif file to be in >"
# e.g. to pull into the working directory
IMAGE_DIR=$PWD
singularity pull --dir $IMAGE_DIR docker://quay.io/biocontainers/pharokka:1.7.3--pyhdfd78af_0
  • Then to run, you use the same commands but prepended with singularity exec <.sif file> e.g.:
containerImage="$IMAGE_DIR/pharokka_1.7.3--pyhdfd78af_0.sif"
singularity exec $containerImage pharokka.py -h

Source

Alternatively, the development version of pharokka (which may include new, untested features) can be installed manually via github. 

git clone https://github.com/gbouras13/pharokka.git
cd pharokka
pip install -e .
pharokka.py --help

The dependencies found in environment.yml will then need to be installed manually.

For example using conda to install the required dependencies:

conda env create -f environment.yml
conda activate pharokka_env
# assuming you are in the pharokka directory 
# installs pharokka from source
pip install -e .
pharokka.py --help

Database Installation

  • Note v 1.4.0 implements a new database with PHROGs HMM profiles. You will need to update the Pharokka database to use v1.4.0 and higher

To install the pharokka database to the default directory:

install_databases.py -d

If you would like to specify a different database directory (recommended), that can be achieved as follows:

install_databases.py -o <path/to/databse_dir>

If this does not work, you an alternatively download the databases from Zenodo at https://zenodo.org/record/8276347/files/pharokka_v1.4.0_databases.tar.gz and untar the directory in a location of your choice.

If you prefer to use the command line:

wget "https://zenodo.org/record/8276347/files/pharokka_v1.4.0_databases.tar.gz"
tar -xzf pharokka_v1.4.0_databases.tar.gz

which will create a directory called "pharokka_v1.4.0_databases" containing the databases.

Beginner Conda Installation

If you are new to using the command-line, please install conda using the following instructions.

  1. Install Conda - I would recommend miniforge.
  2. Assuming you are using a Linux x86_64 machine (for other architectures, please replace the URL with the appropriate one on the miniforge repository).

wget https://github.com/conda-forge/miniforge/releases/download/24.9.2-0/Miniforge3-24.9.2-0-Linux-x86_64.sh

For Mac Intel:

wget https://github.com/conda-forge/miniforge/releases/download/24.9.2-0/Miniforge3-24.9.2-0-MacOSX-x86_64.sh

For Mac M1/M2/M3/M4

wget https://github.com/conda-forge/miniforge/releases/download/24.9.2-0/Miniforge3-24.9.2-0-MacOSX-arm64.sh

  1. Install miniforge and follow the prompts.

sh Miniforge3-24.9.2-0-Linux-x86_64.sh

  1. After installation is complete, you should add the following channels to your conda configuration:
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
  1. Finally, I would recommend installing pharokka into a fresh environment. For example to create an environment called pharokkaENV with pharokka installed:
conda create -n pharokkaENV pharokka
conda activate pharokkaENV
install_databases.py -h
pharokka.py -h

If you have a Mac with Apple Silicon (M1-M4), try

conda create --platform osx-64 -n pharokkaENV pharokka
conda activate pharokkaENV
install_databases.py -h
pharokka.py -h