ALFATClust | Biological sequence clustering tool with dynamic threshold | Genomics library

Method 1: Docker ALFATClust is available as a Docker package, from which a Docker image can be built and then use it to create a Docker container as a virtual environment. Details of Docker and its installation can be found here. Step 1: The Docker image can be built via either the repository URL or the local directory:.
Method 1: Docker ALFATClust is available as a Docker package, from which a Docker image can be built and then use it to create a Docker container as a virtual environment. Details of Docker and its installation can be found here. Step 1: The Docker image can be built via either the repository URL or the local directory: Option 1: Build with repository URL The following command builds a Docker image managed by the host Docker engine: docker build -t <image name> github.com/phglab/ALFATClust The Docker image built will be named as <image name>. Users may name their own images such as "phglab/alfatclust". Option 2: Build locally Image can also be built after cloning or downloading the ALFATClust repository to local directory: docker build -t <image name> <path of dockerfile> <path of dockerfile> locates the file path of "Dockerfile". If the current path is the root directory of ALFATClust (i.e. the original parent directory of Dockerfile), just specify "." for it. Step 2: Once the image is built, a Docker container can be created from it: docker run -it --mount type=bind,src=<path of host data directory>,dst=<path of container data directory> --name <container name> <image name> A directory (specified in <path of host data directory>) on the host machine can be mounted to the Docker container as <path of container data directory>. An absolute (full) path is recommended. Users may also name their own containers such as "alfatclust". <image name> is the Docker image named in step 1. Refer to here for more mounting options. Step 3: To start an existing container: docker start -ai <container name> <container name> is the Docker container named in step 2. Step 4: To exit the container, run the following command in the terminal running it: exit
Method 2: conda Machines having Miniconda or Anaconda installed can set up a conda environment to run ALFATClust. Step 1: Update conda to the latest version, e.g. for Miniconda it can be updated via terminal: conda update conda Step 2: Create a new conda environment for ALFATClust execution using the environment file "alfatclust-conda.yml": conda env create -n <environment name> --file <path of alfatclust-conda.yml> The conda environment created will be named as <environment name>. Users may name their own environments such as "alfatclust_env". <alfatclust-conda.yml> is located under the root directory of ALFATClust. Step 3: Activate the created conda environment by: conda activate <environment name> <environment name> is the environment named in step 2. Step 4: To deactivate (exit) the conda environment, run the following command: conda deactivate
Method 3: Direct execution in host The source codes of ALFATClust are under the directory "main". Simply copy the contents in the "main" folder to a local folder. Users may consider adding the path of this local folder to PATH variable. Also, make sure the following tools and libraries are properly installed and can be invoked by ALFATClust. The version tested is indicated in parentheses. Python runtime: Python 3 (3.7.1) Python packages: numpy (1.20.1) scipy (1.6.0) pandas (1.2.2) biopython (1.78) python-igraph (0.8.3) leidenalg (0.8.3) Third-party tool: Mash (2.2.2) MMseqs2 (12.113e3)