Installation

Currently Autometa package installation is supported by mamba, and docker. For installation using mamba, download mamba from Mambaforge.

Attention

If you are only trying to run the Autometa workflow, you should start at Getting Started before proceeding.

Direct installation (Quickest)

1. Install mamba

   wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
   bash Mambaforge-$(uname)-$(uname -m).sh
   

   Follow the installation prompts and when you get to this:

   Do you wish the installer to initialize Mambaforge
   by running conda init? [yes|no]
   [no] >>> yes
   

   This will require restarting the terminal, or resetting the terminal with the source command

   # To resolve the comment:
   # ==> For changes to take effect, close and re-open your current shell. <==
   # type:
   source ~/.bashrc
   

   Note

   If you already have conda installed, you can install mamba as a drop-in replacement.

   conda -n base -c conda-forge mamba -y
   

2. Create a new environment with autometa installed:

   mamba create -c conda-forge -c bioconda -n autometa autometa
   

   Note

   You may add the bioconda and conda-forge channels to your mamba config to simplify the command.

   mamba config --append channels bioconda
   mamba config --append channels conda-forge
   

   Now mamba will search the bioconda and conda-forge channels alongside the defaults channel.

   mamba create -n autometa autometa
   

3. Activate autometa environment:

   mamba activate autometa
   

Install from source (using make)

Download and install mamba. Now run the following commands:

# Navigate to the directory where you would like to clone Autometa
cd $HOME

# Clone the Autometa repository
git clone https://github.com/KwanLab/Autometa.git

# Navigate into the cloned repository
cd Autometa

# create autometa mamba environment
make create_environment

# activate autometa mamba environment
mamba activate autometa

# install autometa source code in autometa environment
make install

Note

You can see a list of all available make commands by running make without any other arguments.

Install from source (full commands)

Download and install mamba. Now run the following commands:

# Navigate to the directory where you would like to clone Autometa
cd $HOME

# Clone the Autometa repository
git clone https://github.com/KwanLab/Autometa.git

# Navigate into the cloned repository
cd Autometa

# Construct the autometa environment from autometa-env.yml
mamba env create --file=autometa-env.yml

# Activate environment
mamba activate autometa

# Install the autometa code base from source
python -m pip install . --ignore-installed --no-deps -vv

Building the Docker image

You can build a docker image for your clone of the Autometa repository.

1. Install Docker

2. Run the following commands

# Navigate to the directory where you need to clone Autometa
cd $HOME

# Clone the Autometa repository
git clone https://github.com/KwanLab/Autometa.git

# Navigate into the cloned repository
cd Autometa

# This will tag the image as jasonkwan/autometa:<your current branch>
make image

# (or the full command from within the Autometa repo)
docker build . -t jasonkwan/autometa:`git branch --show-current`

Testing Autometa

You can also check the installation using autometa’s built-in unit tests. This is not at all necessary and is primarily meant for development and debugging purposes. To run the tests, however, you’ll first need to install the following packages and download the test dataset.

# Activate your autometa mamba environment
mamba activate autometa

# List all make options
make

# Install dependencies for test environment
make test_environment

# Download test_data.json for unit testing to tests/data/
make unit_test_data_download

You can now run different unit tests using the following commands:

# Run all unit tests
make unit_test

# Run unit tests marked with entrypoint
make unit_test_entrypoints

# Run unit tests marked with WIP
make unit_test_wip

Note

As a shortcut you can also create the test environment and run all the unit tests using make unit_test command.

For more information about the above commands see the Contributing Guidelines page. Additional unit tests are provided in the test directory. These are designed to aid in future development of autometa.