Installation

Install moth

To install moth via pypi, run (only test-pypi yet):

user@computer:~$ pip install -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple moth

Install QuPath

To interact with QuPath, paquo (package that moth extends) requires a working QuPath installation. To install QuPath follow the QuPath installation guide: Install QuPath.

If QuPath is not installed in the default directory, you need to configure QuPath for paquo via:

use via enviroment variable
user@computer:~$ export PAQUO_QUPATH_DIR=/path/to/QuPath

or via the configuration of paquo

Install via Docker

To get a ready to use (python, moth and QuPath installed) Docker container, clone the repository and use the Dockerfile from github to create a new Docker image.

To use the Dockerfile follow the below steps for creating an image:

user@computer:~/path/to/the/repository$ docker build [-t tagname] .

now you can run the container using:

user@computer:~/path/to/the/repository$ docker run -it tagname bash

To mount files or data, explore the docker run documentation

Visual Studio Code Dev Container

If you want to use a VSCode Dev Container, copy the Dockerfile to the directory you want to work with. Open the folder in VSCode and follow the VSCode Dev Container Guide