sc2-sequencing/illumina/README.md

# Illumina

## FASTQ Downloader

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/sc2-sequencing.git
    cp sc2-sequencing/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

## FASTQ Sorters

These scripts change the file names of the FASTQ files to correspond with the
well positions during prep phases.

### Usage

To be run with Julia.

```powershell
julia --project=PATH_TO_ILLUMINA_FOLDER PATH_TO_SORTING_SCRIPT
```

In practice, this looks like

```powershell
julia --project=C:\Users\MillironX\illumina C:\Users\MillironX\illumina\sort-miseq.jl
```

### Installation

These scripts require [Julia](https://julialang.org).

1. Download and install Julia
    1. Select "Add Julia to PATH" as an option
    2. All other default options will work
2. Download the Repo's ZIP file (click green button on upper-right)
3. Press `Win+R`, type `%USERPROFILE%` and press Enter
4. Copy the illumina folder from the ZIP file into the newly opened folder
5. Press `Win+X`, then `I` to open a new PowerShell window
6. Type `julia --project=$env:USERPROFILE\illumina` and press Enter
7. Press the `]` key, the prompt should change to say `(illumina) pkg>`
8. Run `instantiate`
9. Press the backspace key to return to the `julia>` prompt
10. Run `exit()`
11. Close PowerShell
12. Right-click the Windows desktop, and click "New | Shortcut..."
13. Type `julia --project=%USERPROFILE%\illumina
    %USERPROFILE%\illumina\sort-miseq.jl` and click Next
14. Type `Sort MiSeq Run` or something else memorable and click "Finish"
15. Right-click the Windows desktop, and click "New | Shortcut..."
16. Type `julia --project=%USERPROFILE%\illumina
    %USERPROFILE%\illumina\sort-nextseq.jl` and click Next
17. Type `Sort NextSeq Run` or something else memorable and click "Finish"