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github

Installation

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

Herein ‘PipeCraft’ == ‘PipeCraft2’. Using those interchangeably.

Prerequisites

The only prerequisite is Docker.

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

Note

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.

Warning

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

Windows

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

  1. Download PipeCraft2 for Windows: v1.0.0

  2. Install PipeCraft2 via the setup executable

  3. Download Docker for windows - ONLY ONCE (no need, when updating PipeCraft)

Warning

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).

Note

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). Default = 50% of total memory on Windows or 8GB, whichever is less. 80% of total memory on Windows on builds before 20175 (Win10, from 2020).

Quick guide to increase Docker accessible RAM size in Windows

Instructions from https://learn.microsoft.com/en-us/windows/wsl/wsl-config#wslconfig

  1. This is for Windows Build 19041 and later with WSL 2

  2. Open ‘File Explorer’ and type %USERPROFILE% to the address bar to access the %USERPROFILE% directory (generally e.g. “C:Usersmy_user_name”).

  3. Make new text (txt) document into %USERPROFILE% directory.

  4. Paste the following text to that new txt document:

make .wslconfig file
 # Settings apply across all Linux distros running on WSL 2
 [wsl2]

 # Limits VM memory to use no more than X GB, this can be set as whole numbers using GB or MB
 memory=30GB

 # Sets the VM to use X virtual processors
 processors=8

  1. Edit “memory=30GB” and “processors=8” according to your needs

  2. Save the file and rename this as .wslconfig

  3. Restart Docker.

MacOS

PipeCraft2 is supported on macOS 10.15+. Older OS versions might not support PipeCraft GUI workflow through Docker.

Note

If your MacOS has M1/M2 chips, please let us know if you encounter something weird while trying to run some analyses (contact or post an issue on the github page).

  1. Download PipeCraft2 for Mac: v1.0.0

  2. Install PipeCraft2 via pkg file

  3. Currently macOS will flag pipecraft as an 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. Installing on latest versions of macOS (13.0+) will require you to disable gatekeeper entirely, to do so paste the following command into a terminal.

  4. Check your Mac chip (Apple or Intel) and download Docker for Mac - ONLY ONCE (no need, when updating PipeCraft)

sudo spctl --master-disable

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

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Note

Manage Docker resource limits in the Docker dashboard: Alternative text

Linux

PipeCraft2 was tested with Ubuntu 20.04 and Mint 20.1. Older OS versions might not support PipeCraft GUI workflow through Docker.

  1. Download PipeCraft2 for Linux: v1.0.0

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

  3. Install Docker - ONLY ONCE (no need, when updating PipeCraft); follow the guidelines under appropriate Linux distribution

    Warning

    When installing Docker Engine, make sure you have not Docker Desktop already installed!
    Installing both might have interfering consequences

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

Note

When you encounter ERROR during PipeCraft2 installation, then uninstall the previous version of PipeCraft2 sudo dpkg --remove pipecraft-v0.1.3

  1. Run PipeCraft2. If PipeCraft shortcut does not appear on the Desktop, then search the app and generate shortcut manually (installed in /opt/pipecraft directory)

Note

On Linux, Docker can use all available host resources.

Updating PipeCraft2

Auto-updates will be available (hopefully) soon [at least for Windows]!

Warning

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 v1.0.0, if docker container is updated for the new PipeCraft2 version, then it will get a new tag; so, no need to purge all previous docker containers (but to save disk space, see which containers you have not used for a while and perhaps delete those)

Uninstalling PipeCraft2

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

Purging ‘old’ Docker installations

To uninstall docker engine and all its packages:
 sudo apt-get purge docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin docker-ce-rootless-extras
To uninstall docker desktop and clean configurations:
    rm -r $HOME/.docker/desktop
    sudo rm /usr/local/bin/com.docker.cli
    sudo apt purge docker-desktop

Removing Docker images

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

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On Linux machines: containers and images are managed via the Docker cli commands (https://docs.docker.com/engine/reference/commandline/rmi/):
sudo docker images –> to see which docker images exist
sudo docker rmi IMAGE_ID –> to delete selected image

or

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