# Illumina

This script downloads all FASTQs associated with a specific Run ID from
Illumina's Basespace.

## Usage

To be run in Cygwin

```bash
dl-fastqs.sh
```

The script will prompt for a Run ID. Copy the Run ID from the URL in Illumina
Basespace.

![Illumina
Basespace](https://user-images.githubusercontent.com/25492070/113320967-59a88000-92d0-11eb-967c-6b338e247ca5.png)

Note that Ctrl+V does not paste in either Cygwin or Windows terminals. Use
right-click, instead.

## Installation

This script requires [Cygwin](https://cygwin.com/install.html). The install
process is complicated thanks to requiring native features of both Windows and
Cygwin.

1. Download and install Cygwin
    1. Select "Just Me" when asked who to install for
    2. Find and add the latest version of the "git" packages
    3. All other default options will work
2. Press `Win+X`, then `I` to open a new PowerShell window
3. Run `wget
   'https://api.bintray.com/content/basespace/BaseSpaceCLI-EarlyAccess-BIN/latest/\$latest/amd64-windows/bs.exe?bt_package=latest'
   -O $env:LOCALAPPDATA\Microsoft\WindowsApps\bs.exe`
4. Close PowerShell
5. Open Cygwin Console and run

    ```bash
    BS=$(cygpath "C:\Users\\$USER\AppData\Local\Microsoft\WindowsApps\bs.exe")
    $BS auth
    ```

6. Copy the given link, navigate to it in a browser, and login to Illumina
   Basespace
7. In Cygwin console now run

    ```bash
    git clone https://github.com/MillironX/wphl-bioinformatics.git
    cp wphl-bioinformatics/illumina/dl-fastqs.sh ~
    chmod +x dl-fastqs.sh
    ```

8. Right-click the Windows desktop, and click "New | Shortcut..."
9. Type `C:\cygwin64\bin\bash.exe` and click Next
10. Type `Download Illumina Run` or something else memorable and click "Finish"
11. Right-click the newly created shortcut and click Properties
12. In the Target textbox, add a space and `--login dl-fastqs.sh` to the
    existing text
13. Click OK