Table of Contents

  1. Installation
    1. Conda
    2. AlleleFinder
  2. Tests

Installation

AlleleFinder is available as a conda package. Therefore, conda must be installed on your system.

Conda

Skip this step if you have already installed conda.

```bash wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; bash miniconda.sh -b -p $HOME/miniconda conda update -q conda ```

AlleleFinder

You can now install the AlleleFinder package:

I prefer to create a new conda environment and install the AlleleFinder in a single step:

conda create -n allelefinder -c olc-bioinformatics allelefinder

If you wish to create an environment separately:

conda create -n allelefinder python=3.9

You can now install AlleleFinder into this environment:

conda activate allelefinder
conda install -c olcbioinformatics allelefinder

If you don't have the ability to install conda for whatever reason, you can install the software with pip.

You'll need a virtual environment with Python 3.9 (start at the appropriate place in these directions depending on your setup):

(if you don't have Python)

sudo apt install python3

(if you don't have pip)

sudo apt install python3-pip

(if you don't have virtualenv)

pip install virtualenv

Create a Python 3.9 virtual environment:

python3.9 -m venv allelefinder

Activate the environment:

source allelefinder/bin/activate

Install AlleleFinder

pip install allelefinder

You'll also need to install the dependencies. You can do this using the requirements.txt file:

pip install -r requirements.txt

To check the installed version of AlleleFinder, use the following command:

pip show allelefinder | grep Version

Tests

If you encounter issues with the AlleleFinder package, tests are available to ensure that the installation was successful and the basic functionality is present.

You will need to clone this repository and run the tests with pytest. Note: for whatever reason, you need to include the -s flag, or you will get an INTERNALERROR> OSError: [Errno 9] Bad file descriptor error

Running Tests

To ensure that AlleleFinder is working correctly, you can run a set of tests. Here's how to do it:

  1. Clone the AlleleFinder repository from GitHub. This will create a copy of the repository on your local machine.

    bash git clone https://github.com/OLC-Bioinformatics/AlleleFinder.git

  2. Navigate into the cloned repository. This is where the test files are located.

    bash cd AlleleFinder

  3. Run the tests using pytest. The -m option tells Python to run the library module as a script, invoking the module's __main__ function.

    The --cov=allele_tools/ option is used to measure code coverage of the allele_tools module.

    The --cov-config=.coveragerc option specifies the configuration file for coverage.

    The --cov-report term-missing option generates a report in the terminal showing lines missed.

    The -s option disables all capturing of stdout and stderr by pytest. This means that you can see the print statements from the tests in the console.

    The -vvv option increases verbosity. Pytest will give more detailed output, including all test names and the results for each test.

    bash python -m pytest tests/ --cov=allele_tools/ --cov-config=.coveragerc --cov-report term-missing -s -vvv