Arvados Common Workflow Language runner
Project description
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.
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