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Add sorting scripts to Illumina README

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This commit is contained in:
Thomas A. Christensen II 2021-04-13 13:52:23 -06:00
parent 54b8fddca8
commit 8bc8362a62
Signed by: millironx
GPG key ID: 139C07724802BC5D
2 changed files with 50 additions and 2 deletions
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1
.vscode/settings.json vendored
View file

@ -4,6 +4,7 @@
"chmod",
"cygpath",
"demux",
"miseq",
"mkdir",
"wphl"
]

51
illumina/README.md
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@ -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"