Dockerization

[straussmaximilian]

This is to collect all docker-related issues.

Status

There are two experimental dockerfiles Dockerfile_bruker and Dockerfile_thermo.

Dockerfile_bruker is so far not finished. There is a split for two dockerfiles as it was quite challenging to be compatible, on the Thermo side we need the mono installation and on the Bruker side we need a recent Ubuntu version for the feature finder.

The Dockerfile_thermo builds, however behaves not very stable. It stops at random points (e.g. for Thermo in feature finding) , even for very small files. The UI remains stable. I suspect that these issues seem to be process related. Any help is welcome.

Legacy description

There was a previous description in the readme which is removed until docker is tested.

---

Dockerization

We provide a dockerfile to show how to run AlphaPept in a containerized environment. This allows building powerful pipelines e.g. with AWS Batch. The dockerfile will launch the browser-based GUI.

1. Install docker
2. Build the dockerfile with docker build -t docker-alphapept:latest . This took approximately ~10 minutes on a 2019 MacBookPro)
3. Run the container docker run -p 8501:8501 -v /Users/mstrauss/Desktop/docker:/home/alphapept/ docker-alphapept:latest alphapept gui

Notes: -p 8501:8501 forwards the streamlit port to the same port on your machine. You can access AlphaPept via localhost:8501 -v /Users/mstrauss/Desktop/docker:/shared_folder/ mounts the volume to your docker container. E.g., in this case, the local docker-folder on the Desktop can be accessed via /shared_folder/.

---