If you have git installed, then go to the directory of your choice and run the following commands :
git clone https://gitlab.com/fordead/fordead_package.git cd fordead_package
Or without git, simply download and unzip the package from the gitlab page
If you have the anaconda python distribution installed, simply run the following commands from the command prompt in the directory of the package :
conda env create --name fordead_env conda activate fordead_env pip install .
The conda environment can be deleted using the following command :
conda env remove -n fordead_env
Install without conda
If you don't have conda, you can find the required dependencies in the environment.yml file and install them by hand before running the following command in the package directory :
pip install .
It is also possible to use this package using a docker. The docker image associated with this package already includes a conda environment with python and required dependencies, allowing to run containers in which to use this package. To use this docker image, if you are on windows, you must first install Docker Desktop.
Then use the following command to pull the docker image from this package's gitlab page.
docker pull registry.gitlab.com/fordead/fordead_package
Now you can create a container from the command line. By default docker containers can't access your directories, for it to be able to read and write data, you must specify a directory with all necessary data, the fordead package, and planned output directories.
docker run -t -i --name MYCONTAINER -v <YOUR_WORKING_DIRECTORY>:/mnt registry.gitlab.com/fordead/fordead_package /bin/bash
The contents of this working directory will be available in the "/mnt" directory inside the container. For example, if you have the directory "E:/fordead/fordead_package", and you use the command
docker run -t -i --name fordead -v E:/fordead:/mnt registry.gitlab.com/fordead/fordead_package /bin/bash, its absolute path will then be "/mnt/fordead_package" in the container.
Then activate the virtual environment containing all dependencies, and install the fordead package.
conda activate fordead cd <your_fordead_package_directory> pip install .
You can now use all of fordead's command line functions or run python scripts using fordead functions from there.
When you are done, you can stop the container using
docker stop fordead.
If you wish to work using this container again, it is already created and already has fordead installed, and you can simply use :
docker start MYCONTAINER docker exec -it MYCONTAINER /bin/bash
You can detach from the container using CTRL-D, and reattach or attach several times to access it with multiple command lines using
docker exec -it MYCONTAINER /bin/bash.