lega-commander

README

lega-commander

Installation / Update

Manual Installation (Linux/macOS)

1. Download the appropriate tarball for your operating system from the releases page.
2. (Optional) Verify the file’s checksum using the checksum file provided in the same release.
3. Extract the tarball (e.g., tar -xzf <filename>.tar.gz).
4. Move the extracted binary (lega-commander) to a folder in your system’s PATH.

For example:

Option 1: Install system-wide (requires sudo):

sudo cp lega-commander /usr/local/bin/
sudo chmod +x /usr/local/bin/lega-commander

Option 2: Install for the current user (no sudo required):

mkdir -p ~/.local/bin
cp lega-commander ~/.local/bin/
chmod +x ~/.local/bin/lega-commander

Note: Ensure ~/.local/bin is in your PATH.

Windows

Go to the releases page and manually download the latest binary. Double-click the .zip (if provided) to extract it, and then place lega-commander.exe in your desired location (for example, in C:\Program Files\ or another folder included in your PATH).

Automated Installation

Linux

Run the command below on your terminal:

curl -fsSL https://raw.githubusercontent.com/ELIXIR-NO/FEGA-Norway/main/cli/lega-commander/install.sh | sudo sh

MacOS

Run the command below on your terminal:

curl -fsSL https://raw.githubusercontent.com/ELIXIR-NO/FEGA-Norway/main/cli/lega-commander/install.sh | sh

This script:

1. Detects your OS and architecture.
2. Fetches the latest (or specified) version of lega-commander from the GitHub releases.
3. Verifies the downloaded binary against a checksum to ensure integrity.
4. Extracts the binary and installs it to a suitable system directory (e.g., /usr/local/bin or $HOME/.local/bin).
5. Removes temporary files and confirms a successful installation.

Advanced Installation Options

The installation script (install.sh) provides several options to customize the installation process.

Usage: $this [-b bindir] [-t tag] [-d] [-h]
  -b  Sets bindir or installation directory (defaults to /usr/local/bin).
  -t  Sets a specific tag (e.g., "vX.Y.Z") to install.
  -d  Turns on debug logging (if available).
  -h  Displays this help message.

If no tag is specified, the latest release from:
  https://github.com/ELIXIR-NO/FEGA-Norway/releases
will be installed.

Configuration

Before using the lega commander, make sure all the environment variables required for authentication are set:

In linux and MacOS you can use below commands in commandlines to set them:

export CENTRAL_EGA_USERNAME=...
export CENTRAL_EGA_PASSWORD=...
export ELIXIR_AAI_TOKEN=...

In windows, the variables must be set in environmental variables list.(Explained here)

Table below shows how there variables must be set:

Environmental variable name	description
CENTRAL_EGA_USERNAME	The user name that you received from CEGA website
CENTRAL_EGA_PASSWORD	The password that you received from CEGA website
ELIXIR_AAI_TOKEN	The token that you received after login here:(https://ega.elixir.no/)

for developers: the tool is pre-configured to work with Norwegian Federated EGA instance: https://ega.elixir.no. If you want to specify another instance, you can set LOCAL_EGA_INSTANCE_URL environment variable.

Usage

For the time being, all of upload and download commands should not run with -b argument.

$ lega-commander
lega-commander [inbox | outbox | resumables | upload | download] <args>

 inbox:
  -l, --list    Lists uploaded files
  -d, --delete= Deletes uploaded file by name

 outbox:
  -l, --list  Lists exported files

 resumables:
  -l, --list    Lists resumable uploads
  -d, --delete= Deletes resumable upload by ID

 upload:
  -f, --file=FILE or =FOLDER    File or folder to upload
  -r, --resume                  Resumes interrupted upload
  -b, --beta                    Upload the files without the proxy service;i.e. directly to tsd file api. This means the parts of the file are sent to tsd file api instead of sending them to proxy service and then proxy service forward them to tsd file api. So it would be one-part transferring instead of two-part transferring.

 download:
  -f, --file= FILE or =FOLDER   File or folder to download

Example Usage

As an example, if we want to upload file named sample-c4gh-file.c4gh and in path of /path/to/a/c4gh/file or D:\path\to\a\c4gh\file, we wil do it with commands below based on operating system:

In linux or macos:

lega-commander upload   -f /path/to/a/c4gh/file/sample-c4gh-file.c4gh 

In windows (in the case that lega-commander binary [dowloaded from release page] is in D:\users\lega-commander folder):

D:\users\lega-commander upload  -f D:\path\to\a\c4gh\file\sample-c4gh-file.c4gh 

or if we want to upload a folder with path of /path/to/a/folder/containing/c4gh/files that contains c4gh files, we can use this example command:

lega-commander upload  -f /path/to/a/folder/containing/c4gh/files

Documentation

Overview

Package main is the main package of lega-commander command-line tool, containing "files", "resumables" and "uploads" commands implementations along with additional helper methods.