mirror of
https://github.com/MillironX/sc2-sequencing.git
synced 2024-12-22 11:18:17 +00:00
Correct and cleanup Illumina README
This commit is contained in:
parent
a2a86ae788
commit
befca3557e
2 changed files with 37 additions and 22 deletions
7
.vscode/settings.json
vendored
Normal file
7
.vscode/settings.json
vendored
Normal file
|
@ -0,0 +1,7 @@
|
||||||
|
{
|
||||||
|
"cSpell.words": [
|
||||||
|
"chmod",
|
||||||
|
"cygpath",
|
||||||
|
"wphl"
|
||||||
|
]
|
||||||
|
}
|
|
@ -1,53 +1,61 @@
|
||||||
# Illumina
|
# 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
|
## Usage
|
||||||
|
|
||||||
To be run in Cygwin
|
To be run in Cygwin
|
||||||
|
|
||||||
```bash
|
```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
|
## 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. Download and install Cygwin
|
||||||
1. Select "Just Me" when asked who to install for
|
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
|
3. All other default options will work
|
||||||
2. Press `Win+X`, then `I` to open a new PowerShell window
|
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
|
4. Close PowerShell
|
||||||
5. Open Cygwin Console and run
|
5. Open Cygwin Console and run
|
||||||
|
|
||||||
```bash
|
```bash
|
||||||
$ BS=$(cygpath "C:\Users\\$USER\AppData\Local\Microsoft\WindowsApps\bs.exe")
|
BS=$(cygpath "C:\Users\\$USER\AppData\Local\Microsoft\WindowsApps\bs.exe")
|
||||||
$ $BS auth
|
$BS auth
|
||||||
```
|
```
|
||||||
6. Copy the given link, navigate to it in a browser, and login to Illumina Basespace
|
|
||||||
|
6. Copy the given link, navigate to it in a browser, and login to Illumina
|
||||||
|
Basespace
|
||||||
7. In Cygwin console now run
|
7. In Cygwin console now run
|
||||||
|
|
||||||
```bash
|
```bash
|
||||||
$ git clone https://github.com/MillironX/wphl-bioinformatics.git
|
git clone https://github.com/MillironX/wphl-bioinformatics.git
|
||||||
$ cp wphl-bioinformatics/illumina/dl-fastqs.sh ~
|
cp wphl-bioinformatics/illumina/dl-fastqs.sh ~
|
||||||
$ chmod +x dl-fastqs.sh
|
chmod +x dl-fastqs.sh
|
||||||
```
|
```
|
||||||
|
|
||||||
8. Right-click the Windows desktop, and click "New | Shortcut..."
|
8. Right-click the Windows desktop, and click "New | Shortcut..."
|
||||||
9. Type `C:\cygwin64\bin\bash.exe` and click Next
|
9. Type `C:\cygwin64\bin\bash.exe` and click Next
|
||||||
10. Type `Download Illumina Run` or something else memorable and click "Finish"
|
10. Type `Download Illumina Run` or something else memorable and click "Finish"
|
||||||
11. Right-click the newly created shortcut and click Properties
|
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
|
13. Click OK
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
Loading…
Reference in a new issue