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Correct and cleanup Illumina README

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Thomas A. Christensen II 2021-04-13 12:50:14 -06:00
parent a2a86ae788
commit befca3557e
Signed by: millironx
GPG key ID: 139C07724802BC5D
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{
"cSpell.words": [
"chmod",
"cygpath",
"wphl"
]
}

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illumina/README.md
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# Illumina
This script downloads all FASTQs associated with a specific Run ID from Illumina's Basespace.
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
dl-fastqs.sh
```
The script will prompt for a Run ID. Copy the Run ID from the URL in Illumina Basespace.
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)
![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.
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.
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
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`
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")
$ $BS auth
```
6. Copy the given link, navigate to it in a browser, and login to Illumina Basespace
```bash
BS=$(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
```
```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
12. In the Target textbox, add a space and `--login dl-fastqs.sh` to the
existing text
13. Click OK