diff --git a/.vscode/settings.json b/.vscode/settings.json index 5e5f816..e190e43 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -4,6 +4,7 @@ "chmod", "cygpath", "demux", + "miseq", "mkdir", "wphl" ] diff --git a/illumina/README.md b/illumina/README.md index 3888cac..1a07b28 100644 --- a/illumina/README.md +++ b/illumina/README.md @@ -1,9 +1,11 @@ # Illumina +## FASTQ Downloader + This script downloads all FASTQs associated with a specific Run ID from Illumina's Basespace. -## Usage +### Usage To be run in Cygwin @@ -20,7 +22,7 @@ Basespace](https://user-images.githubusercontent.com/25492070/113320967-59a88000 Note that Ctrl+V does not paste in either Cygwin or Windows terminals. Use right-click, instead. -## Installation +### Installation This script requires [Cygwin](https://cygwin.com/install.html). The install process is complicated thanks to requiring native features of both Windows and @@ -59,3 +61,48 @@ Cygwin. 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"