sc2-sequencing/illumina

Illumina

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

Usage

To be run in Cygwin

dl-fastqs.sh

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

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

Installation

This script requires Cygwin. 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

   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

   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