arvados-cwl-runner 3.1.2

Arvados Common Workflow Language runner

Overview

This package provides the arvados-cwl-runner tool to register and run Common Workflow Language workflows in Arvados.

Installation

Installing under your user account

This method lets you install the package without root access. However, other users on the same system will need to reconfigure their shell in order to be able to use it. Run the following to install the package in an environment at ~/arvclients:

python3 -m venv ~/arvclients
~/arvclients/bin/pip install arvados-cwl-runner

Command line tools will be installed under ~/arvclients/bin. You can test one by running:

~/arvclients/bin/arvados-cwl-runner --version

You can run these tools by specifying the full path every time, or you can add the directory to your shell’s search path by running:

export PATH="$PATH:$HOME/arvclients/bin"

You can make this search path change permanent by adding this command to your shell’s configuration, for example ~/.bashrc if you’re using bash. You can test the change by running:

arvados-cwl-runner --version

Installing on Debian and Ubuntu systems

Arvados publishes packages for Debian 11 “bullseye,” Debian 12 “bookworm,” Ubuntu 20.04 “focal,” and Ubuntu 22.04 “jammy.” You can install the Python SDK package on any of these distributions by running the following commands:

sudo install -d /etc/apt/keyrings
sudo curl -fsSL -o /etc/apt/keyrings/arvados.asc https://apt.arvados.org/pubkey.gpg
sudo tee /etc/apt/sources.list.d/arvados.sources >/dev/null <<EOF
Types: deb
URIs: https://apt.arvados.org/$(lsb_release -cs)
Suites: $(lsb_release -cs)
Components: main
Signed-by: /etc/apt/keyrings/arvados.asc
EOF
sudo apt update
sudo apt install python3-arvados-cwl-runner

Installing on Red Hat, AlmaLinux, and Rocky Linux

Arvados publishes packages for RHEL 8 and distributions based on it. Note that these packages depend on, and will automatically enable, the Python 3.9 module. You can install the Python SDK package on any of these distributions by running the following commands:

sudo tee /etc/yum.repos.d/arvados.repo >/dev/null <<'EOF'
[arvados]
name=Arvados
baseurl=http://rpm.arvados.org/RHEL/$releasever/os/$basearch/
gpgcheck=1
gpgkey=http://rpm.arvados.org/RHEL/RPM-GPG-KEY-arvados
EOF
sudo dnf install python3-arvados-cwl-runner

Configuration

This client software needs two pieces of information to connect to Arvados: the DNS name of the API server, and an API authorization token. The Arvados user documentation describes how to find this information in the Arvados Workbench, and install it on your system.

Testing and Development

This package is one part of the Arvados source package, and it has integration tests to check interoperability with other Arvados components. Our hacking guide describes how to set up a development environment and run tests.