Flywheel in Command Line

Date: April 3, 2025 1:14 PM

Table of Contents

  1. Flywheel in Command Line
  2. Install Legacy Command Line Interface (CLI)
  3. Beta Command Line Interface (CLI)

Install Legacy Command Line Interface (CLI)

Step 1: Download flywheel command line interface

The flywheel CLI is not able to be downloaded off a package manager like pip. Instead, you download it manually into your computer.

There is an existing instance in the Holmes Lab project space at /projects/f_ah1491_1/analysis_tools/flywheel/linux_amd64/fw

OR, you can download it somewhere locally by following the instructions on this tutorial: Installing the Flywheel CLI Then, copy the filepath to where the flywheel .exe was downloaded into. The

Now try linking to that flywheel instance in your terminal, like:

/projects/f_ah1491_1/analysis_tools/flywheel/linux_amd64/fw --version

If that returns a version number, you have it set up correctly.

To use fw commands, you can either:

OPTION 1: Reference flywheel from the full path

This is already set up. You can call the full path to the shared copy of the file (/projects/f_ah1491_1/analysis_tools/flywheel/linux_amd64/fw) each time you want to run a command

/projects/f_ah1491_1/analysis_tools/flywheel/linux_amd64/fw --help

OPTION 2: Move a copy of the fw file to your /home/netID/bin folder so you only have to say fw to reference the package Run these:

$ cp /projects/f_ah1491_1/analysis_tools/flywheel/linux_amd64/fw ~/bin/
$ chmod +x ~/bin/fw
$ fw --help

If that returns the flywheel help menu, it’s set up correctly.

OPTION 3: Add the path to the flywheel executable to your bashrc file

Run these:

$ export PATH="/projects/f_ah1491_1/analysis_tools/flywheel/linux_amd64:$PATH"
$ source ~/.bashrc
$ fw --help

If that returns the flywheel help menu, it’s set up correctly.

If you get a conda error, try running conda deactivate and then again conda deactivate until you’re fully out of all condas and then try this again

Flywheel Help Menu:

usage: fw [-h]  ...

Flywheel command-line interface

options:
  -h, --help  show this help message and exit

Available commands:
  
    login     Login to a Flywheel instance
    logout    Delete your saved API key
    status    See your current login status
    version   Print CLI version
    cp        Copy a local file to a remote location, or vice-a-versa
    ls        Show remote files
    download  Download a remote file or container
    upload    Upload a local file to a Flywheel container
    export    Export data from Flywheel
    job       [DEPRECATED] Start or manage server jobs
    sync      Sync files from Flywheel to storage
    ingest    Ingest data
    deid      Test your de-identification template or generate a sample template

Step 2: Generate an API key on Flywheel

  1. Go to https://cahbir-flywheel.rutgers.edu/#/projects
  2. Click on your profile picture in the top right > ‘Profile’
  3. Scroll down to ‘Flywheel Access’ and click ‘+ Generate API Key’
  4. Copy API key and save in safe space

Step 3: Add your API key to your .bash_aliases file

  1. Log into Amarel on the terminal with ssh
  2. enter nano ~/.bash_aliases
  3. enter ``alias fwlogin=’/path/to/fw login cahbir-flywheel.rutgers.edu:'` For example, if using the Holmes Lab fw instance: `alias fwlogin='/projects/f_ah1491_1/analysis_tools/flywheel/linux_amd64/fw login cahbir-flywheel.rutgers.edu:`
  4. press control+X → ‘Y’ → ‘Enter’ to save and exit
  5. enter source ~/.bashrc` to update

🚨 Note: when your API key expires, make a new one and update it in your bash_aliases through this process

Step 4: login to CLI with API Key on Flywheel:

  1. If you did step 3, type fwlogin' -> This should return You are now logged in as <Your Name>!

  2. If you did not do step 3, copy and paste this formula into your command line

    #Formula: <filepath to fw> login <yourAPIKey>
#ex: 
/path/to/fw  login cahbir-flywheel.rutgers.edu:<your_API_key>

-> When it logs in, it will say You are now logged in as: <Your Name>!

Usage

To view the available list of commands, run fw -h (^^pasted above). More information about each command can found in the Command References documentation folder.

Getting Help

With any command, you can add -h or –help to get more information. For example, with the ls command we’ll see in the following section:

usage: fw ls [-h] [--config-file CONFIG_FILE | --no-config] [-y] [--ca-certs CA_CERTS] [--timezone TIMEZONE] [--debug | --quiet]
             [--ids] [-a]
             [path]
positional arguments:
  path                  The path to list subfolders and files
options:
  -h, --help            show this help message and exit
  --config-file CONFIG_FILE, -C CONFIG_FILE
                        Specify configuration options via config file
  --no-config           Do NOT load the default configuration file
  -y, --yes             Assume the answer is yes to all prompts
  --ca-certs CA_CERTS   The file to use for SSL Certificate Validation
  --timezone TIMEZONE   Set the effective local timezone for imports
  --debug               Turn on debug logging
  --quiet               Squelch log messages to the console
  --ids                 Display database identifiers
  -a, --all             Show all

Beta Command Line Interface (CLI)

⚙

Prerequisites: The install script requires bash, curl, grep, tar, and shasum (or sha256sum) in order to download, extract, and verify the CLI.

1 – SSH into Amarel command line

ssh netID@amarel.rutgers.edu

2 – Download prerequisites

# latest stable version
curl https://storage.googleapis.com/flywheel-dist/fw-cli/stable/install.sh | sh

By default, fw-beta will be extracted under ~/.fw with all of its dependencies. The installation folder can be customized using the envvar FW_CLI_INSTALL_DIR.

Shell profiles are automatically updated to include fw-beta on the PATH for bash and zsh using ~/.bash_profile and ~/.zshenv respectively.

3 — Activate new bash profile

source ~/.bash_profile

4 — Use CLI export

Export data from a Flywheel project to an external storage.

USAGE
  fw-beta export [OPTIONS] COMMAND [ARGS]...

  Export data from FW to a storage.

COMMANDS
  run       Export data from a project via the connector service
  get       Get export by ID
  list      List exports
  cancel    Cancel an export by ID
  rerun     Rerun an export by ID
  schedule  Schedule exports to run later or repeatedly

OPTIONS--docs  Show HTML docs for command
  --help  Show this message and exit