SQ meetings - CI and Docker workshop (01/04/2022)

Prerequisites

• Python 3.8 or newer
• Docker
• git
• A GitHub account (required for the CI part)
• A text editor
• Apptainer/Singularity (optional)
• pipeviewer (pv, optional)

The code in this repository was developed on a Linux machine and should run fine on macOS. The code should in principle run on Windows. Nevertheless, a laptop with a UNIX-like os is highly recommended.

Singularity has recently been renamed to Apptainer. First try to install Apptainer and fall back on Singularity if Apptainer is not available for your OS/distribution.

Installing Docker

If you are running a Linux distribution you can most likely install Docker through your system package manager (è.g. apt, dnf, pacman...).

In case your distribution does not package Docker, you can try to follow these instructions.

On macOS the instructions vary sligthly depending on whether you device has an Apple Silicon (M1) CPU:

• Instructions for macOS w/ Intel CPUs - link
• Instructions for macOS w/ Apple Silicon - link

Here are the instructions for Windows in case you don't have access to a laptop with Linux/macOS: link If you are running macOS

Installing Apptainer/Singularity

Apptainer/Singularity can only run on Linux. If you are using macOS or Windows feel free to skip this section.

Many Linux distributions have a package for Apptainer/Singularity.

In case yours doesn't, you can follow these instructions to install Apptainer from source.

Testing Docker and Apptainer/Singularity

Testing Docker:

sudo docker run ubuntu:20.04 cat /etc/os-release

Testing Apptainer/Singularity:

singularity exec docker://ubuntu:20.04 cat /etc/os-release

Both commands should produce an output like the following:

NAME="Ubuntu"
VERSION="20.04.4 LTS (Focal Fossa)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 20.04.4 LTS"
VERSION_ID="20.04"
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
VERSION_CODENAME=focal
UBUNTU_CODENAME=focal

In case you host machine is running Ubuntu 20.04

If your host machine is running Ubuntu 20.04, you can try to run the above commands with fedora:36 instead of ubuntu:20.04 In this case the output should looke like this:

NAME="Fedora Linux"
VERSION="36 (Container Image Prerelease)"
ID=fedora
VERSION_ID=36
VERSION_CODENAME=""
PLATFORM_ID="platform:f36"
PRETTY_NAME="Fedora Linux 36 (Container Image Prerelease)"
ANSI_COLOR="0;38;2;60;110;180"
LOGO=fedora-logo-icon
CPE_NAME="cpe:/o:fedoraproject:fedora:36"
HOME_URL="https://fedoraproject.org/"
DOCUMENTATION_URL="https://docs.fedoraproject.org/en-US/fedora/f36/system-administrators-guide/"
SUPPORT_URL="https://ask.fedoraproject.org/"
BUG_REPORT_URL="https://bugzilla.redhat.com/"
REDHAT_BUGZILLA_PRODUCT="Fedora"
REDHAT_BUGZILLA_PRODUCT_VERSION=36
REDHAT_SUPPORT_PRODUCT="Fedora"
REDHAT_SUPPORT_PRODUCT_VERSION=36
PRIVACY_POLICY_URL="https://fedoraproject.org/wiki/Legal:PrivacyPolicy"
VARIANT="Container Image"
VARIANT_ID=container

Repository structure

• bedtools_ng/ contains the source files and unit tests for the toy application we will be using throughout the workshop
• snippets/ contains few cheatsheets with common/useful commands
• .github/workflows/ contains two example workflows that will be used as base to develop more complex workflows

GitHub container registry (GHCR)

Packages published on the GHCR for the current repository are available in the Package section on the right:

GitHub actions logs

Logs for GitHub actions runs ara available under the Actions tab in the top bar: