Getting started at the command line

Many operations in Arvados can be performed using either the web Workbench or through command line tools. Some operations can only be done using the command line.

To use the command line tools, you can either log into an Arvados virtual machine where those tools are pre-installed, or install the Arvados tools on your own system.

Option 1: Using an Arvados virtual machine

This is the command line interface we recommend for most day-to-day work, because the tools are all preinstalled and preconfigured for you. You can log in to any virtual machine where you have permission by using:

the Webshell client accessible through Arvados Workbench
Unix SSH clients
Windows SSH clients

Option 2: Installing Arvados tools on your own system

This option gives you more flexibility in your work, but takes more time to set up.

Install client tools on Red Hat, AlmaLinux, and Rocky Linux

Note:

Arvados tools require newer language runtimes than the default versions included with these distributions. These instructions will upgrade language runtimes for the entire system. Check that won’t interfere with any existing software before you proceed.

Set up the Arvados package repository and install the packages by running these commands:

# 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
# dnf module enable python39:3.9
# dnf install arvados-client python3-arvados-python-client python3-arvados-cwl-runner python3-arvados-fuse python3-crunchstat-summary

Proceed to build and install the Arvados CLI tools:

# dnf module enable ruby:3.1
# dnf install ruby ruby-devel gcc-c++ make redhat-rpm-config glibc-devel glibc-headers curl-devel openssl-devel zlib-devel
# gem install arvados-cli

Install client tools on Debian and Ubuntu

Set up the Arvados package repository and install the packages by running these commands:

# install -d /etc/apt/keyrings
# curl -fsSL -o /etc/apt/keyrings/arvados.asc https://apt.arvados.org/pubkey.gpg
# declare $(grep "^VERSION_CODENAME=" /etc/os-release || echo VERSION_CODENAME=MISSING)
# tee /etc/apt/sources.list.d/arvados.sources >/dev/null <<EOF
Types: deb
URIs: https://apt.arvados.org/$VERSION_CODENAME
Suites: $VERSION_CODENAME
Components: main
Signed-by: /etc/apt/keyrings/arvados.asc
EOF
# apt update
# apt install arvados-client python3-arvados-python-client python3-arvados-cwl-runner python3-arvados-fuse python3-crunchstat-summary

Proceed to build and install the Arvados CLI tools:

# apt install ruby ruby-dev gcc g++ make libc-dev libcurl4-openssl-dev zlib1g-dev
# gem install arvados-cli

Proceed to configuration

Once you have the command line tools installed, proceed to getting an API token.

Previous: Processing Whole Genome Sequences Next: Getting an API token