Merge pull request #346 from ELIXIR-NO/feat/update-lega-readme

Add detailed usage explanation for install script options in README

cli/lega-commander/README.md

@@ -2,20 +2,71 @@
 
 ## Installation / Update
 
-### Linux
-run the command below on your terminal:
+### Manual Installation (Linux/macOS)
+
+1. **Download** the appropriate tarball for your operating system from the [releases page](https://github.com/ELIXIR-NO/FEGA-Norway/releases?q=lega-commander-*-assets).
+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](https://github.com/ELIXIR-NO/FEGA-Norway/releases?q=lega-commander-*-assets) 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:
+#### 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
 ```
 
-### Windows
-Go to the [releases page](https://github.com/ELIXIR-NO/FEGA-Norway/releases?q=lega-commander-*-assets) and download the latest binary manually.
+
+
+#### 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:
@@ -89,6 +140,9 @@ that contains c4gh files, we can use this example command:
 ```
 lega-commander upload  -f /path/to/a/folder/containing/c4gh/files
 ```
+
+<!--
 ### How it works
 The flowchart below shows how lega commander connects to the other components of project in order to **UPLOAD** the file/folder:
-![Flowchart of upload](flowchart_lega_commander.jpg)
+![Flowchart of upload](flowchart_lega_commander.jpg)
+-->

cli/lega-commander/install.sh

@@ -7,13 +7,15 @@ usage() {
   cat <<EOF
 $this: Download Go binaries for lega-commander from ELIXIR-NO/FEGA-Norway
 
-Usage: $this [-b] bindir [-d] [tag]
-  -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
-   [tag] is a tag from
-   https://github.com/ELIXIR-NO/FEGA-Norway/releases
-   If tag is missing, then the latest will be used.
+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.
+  -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.
 
 EOF
   exit 2