From 3e8f97f71fa2f0157e975796703ce35ed761f22e Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Thu, 1 Apr 2021 09:59:35 -0600
Subject: [PATCH] Create README.md

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+# 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" and "xargs" 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 ` --login dl-fastqs.sh` (including the space) to the existing text
+13. Click OK
+
+
+