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 conda is taking a long time to solve the environment, try using mamba:
conda install mamba
mamba install -c bioconda pharokka
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.
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/8267900/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.
- Install Anaconda. I would recommend miniconda.
- Assuming you are using a Linux x86_64 machine (for other architectures, please replace the URL with the appropriate one on the miniconda website).
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
For Mac (Intel, will also work with M1):
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
- Install miniconda and follow the prompts.
sh Miniconda3-latest-Linux-x86_64.sh
- 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
- After this, conda should be installed (you may need to restart your terminal). It is recommended that mamba is also installed, as it will solve the enviroment quicker than conda:
conda install mamba
- Finally, I would recommend installing pharokka into a fresh environment. For example to create an environment called pharokkaENV with pharokka installed:
mamba create -n pharokkaENV pharokka
conda activate pharokkaENV
install_databases.py -h
pharokka.py -h