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Containerized Installation

Method 3: Installing from Docker Hub

Pull the latest Docker image from Docker Hub:

docker pull manuelrueda/clarid-tools:latest
docker image tag manuelrueda/clarid-tools:latest cnag/clarid-tools:latest

Method 4: Installing from Dockerfile

Download the Dockerfile from GitHub:

wget https://raw.githubusercontent.com/CNAG-Biomedical-Informatics/clarid-tools/main/docker/Dockerfile

Then build the container:

  • For Docker version 19.03 and above (supports buildx):
docker buildx build -t cnag/clarid-tools:latest .
  • For Docker versions older than 19.03 (no buildx support):
docker build -t cnag/clarid-tools:latest .

Running and Interacting with the Container

To run the container:

docker run -tid -e USERNAME=root --name clarid-tools cnag/clarid-tools:latest

To connect to the container:

docker exec -ti clarid-tools bash

Or, to run directly from the host:

alias clarid-tools='docker exec -ti clarid-tools /usr/share/clarid-tools/bin/clarid-tools'
clarid-tools

System requirements

  • OS/ARCH supported: linux/amd64 and linux/arm64.
  • Ideally a Debian-based distribution (Ubuntu or Mint), but any other (e.g., CentOS, OpenSUSE) should do as well (untested).
  • Perl 5 (>= 5.36 core; installed by default in many Linux distributions). Check the version with perl -v
  • 1GB of RAM
  • >= 1 core (ideally i7 or Xeon).
  • At least 5GB HDD.

Platform Compatibility

This distribution is written in pure Perl and is intended to run on any platform supported by Perl 5. It has been tested on Debian Linux and macOS. It is expected to work on Windows; please report any issues.

Common errors: Symptoms and treatment

  • Dockerfile:
      * DNS errors

    - Error: Temporary failure resolving 'foo'

      Solution: https://askubuntu.com/questions/91543/apt-get-update-fails-to-fetch-files-temporary-failure-resolving-error