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Nils edited this page Jun 25, 2021 · 4 revisions

Downloading needed files

Note that using the pipeline with Docker only works for Linux systems.

Required Software

Download and install the Docker software from the respective website: https://www.docker.com/

Example Docker Images

You can download a running example Docker image here: https://github.com/RUB-Bioinf/HT-PropagatedNeuriteSkeletonization/releases

Make sure to edit the image to include your own user credentials! If you do not do that, you may get permission conflicts.

Running a Docker Image

We recommend to use a provided example docker image and build on it from there! The first step is streamlining your build process. To do this, use this guide to set up a run.sh. Once created, use the terminal to navigate to the directory you saved the file in. Run the file using $ \. run.sh

build.sh

If you want to compile and run the pipeline directly from docker and GitHub, you can create bash scripts to build and run the docker. First, you can create a build.sh with these contents:

docker build . --no-cache --pull --progress tty --force-rm --tag compskel:1.0 && docker run -v </path/to/your/input/directory>:/HT-NeuriteDurixSkSkeletonization/resources -v </path/to/your/output/directory>:/HT-NeuriteDurixSkSkeletonization/output compskel

Note, how this is all a single line input.

If you run this file, it will set up a docker image for you. This image will automatically download all needed libraries (Such as Fiji) and check out the latest version of the master branch. Then it will run the pipelines with the directories you have specified using the -v tags.

run.sh

After setting up the docker image, you can create a run.sh to run the previously built image:

docker run -v </path/to/your/input/directory>:/HT-PropagatedNeuriteSkeletonization/resources -v </path/to/your/output/directory>:/HT-PropagatedNeuriteSkeletonization/output compskel

Make sure to replace all pointy brackets with your own folder paths

Testing the Docker Image

You can download example data from this wiki Page: https://github.com/RUB-Bioinf/HT-PropagatedNeuriteSkeletonization/wiki/Example-Data

Docker Tools

  • docker system prune Removes dangling docker images and clears the cache. Use this if you run into troubles when running the docker file.

  • docker ps -a Displays all the running docker tasks. See the last column for the automatically generated name of your docker task. You can remove that task with docker stop and docker remove. Read up on the docker documentation on your own on how to do this.

Make sure you have permission to run these commands.

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