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Current versions do not work on High Performance Computing (HPC) clusters yet.


The only prerequisite is Docker.

See OS-specific (Windows, Mac, Linux) docker installation guidelines below.


Modules of PipeCraft2 are distributed through Docker containers, which will liberate the users from the struggle to install/compile various software for metabarcoding data analyses. Thus, all processes are run in Docker containers. Relevant Docker container will be automatically downloaded prior the analysis.


Your OS might warn that PipeCraft2 is dangerous software! Please ignore the warning in this case.


PipeCraft2 was tested on Windows 10 and Windows 11. Older Windows versions do not support PipeCraft GUI workflow through Docker.

  1. Download Docker for windows

  2. Download PipeCraft for Windows: v0.1.4

  3. Install PipeCraft via the setup executable


In Windows, please keep you working directory path as short as possible. Maximum path length in Windows is 260 characters. PipeCraft may not be able to work with files, that are buried “deep inside” (i.e. the path is too long).


Resource limits for Docker are managed by Windows; but you can configure limits in a .wslconfig file (see Settings -> Resources on your Docker desktop app)


PipeCraft is supported on macOS 10.15+. Older OS versions might not support PipeCraft GUI workflow through Docker.

  1. Check your Mac chip (Apple or Intel) and download Docker for Mac

  2. Download PipeCraft for Mac: v0.1.4

  3. Install PipeCraft via pkg file

  4. Currently, this app might be identified as app from an unidentified developer. Grant an exception for a blocked app by clicking the “Open Anyway” button in the General panel of Security & Privacy preferences

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  1. Open Docker dashboard: Settings -> Resources -> File Sharing; and add the directory where was installed (it is usually /Appications)

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Manage Docker resource limits in the Docker dashboard: Alternative text


PipeCraft was tested with Ubuntu 20.04 and Mint 20.1. Older OS versions might not support PipeCraft GUI workflow through Docker.

  1. Install Docker; follow the guidelines under appropriate Linux distribution

  2. If you are a non-root user complete these post-install steps

  3. Download PipeCraft for Linux: v0.1.4

  4. Right click on the pipecraft_*.deb file and “Open With GDebi Package Installer” (Install Package) or sudo dpkg -i path_to_deb_file


When you encounter ERROR during installation, then uninstall the previous version of PipeCraft sudo dpkg --remove pipecraft-v0.1.3

  1. Run PipeCraft. If PipeCraft shortcut does not appear on the Desktop, then search the app and generate shortcut manually (installed in /opt/pipecraft directory)


On Linux, Docker can use all available host resources.

Updating PipeCraft2

To avaoid any potential software conflicts from PipeCraft2 v0.1.1 to v0.1.4, all Docker images of older PipeCraft2 version should be removed. Starting from v0.1.5 –> if docker container is updated, it will get a new tag for new PipeCraft2 version

See removing docker images section.


Currently available versions HERE


Windows: uninstall PipeCraft via control panel
MacOS: Move to Bin
Linux: remove pipecraft via Software Manager/Software Centre or via terminal sudo dpkg --remove pipecraft

Removing Docker images

On MacOS and Windows: Docker images and container can be easily managed from the Docker dashboard. For more info visit
See command-line based way below.

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On Linux machines: containers and images are managed via the Docker cli commands (
sudo docker images –> to see which docker images exist
sudo docker rmi IMAGE_ID_here –> to delete selected image


sudo docker system prune -a –> to delete all unused containers, networks, images