diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..840f89a --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,7 @@ +{ + "cSpell.words": [ + "chmod", + "cygpath", + "wphl" + ] +} \ No newline at end of file diff --git a/illumina/README.md b/illumina/README.md index e42b9d1..3888cac 100644 --- a/illumina/README.md +++ b/illumina/README.md @@ -1,53 +1,61 @@ # 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 - - -