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108 lines
3.4 KiB
Markdown
108 lines
3.4 KiB
Markdown
# Illumina
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## FASTQ Downloader
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This script downloads all FASTQs associated with a specific Run ID from
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Illumina's Basespace.
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### Usage
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To be run in Cygwin
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```bash
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dl-fastqs.sh
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```
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The script will prompt for a Run ID. Copy the Run ID from the URL in Illumina
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Basespace.
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Note that Ctrl+V does not paste in either Cygwin or Windows terminals. Use
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right-click, instead.
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### Installation
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This script requires [Cygwin](https://cygwin.com/install.html). The install
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process is complicated thanks to requiring native features of both Windows and
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Cygwin.
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1. Download and install Cygwin
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1. Select "Just Me" when asked who to install for
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2. Find and add the latest version of the "git" packages
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3. All other default options will work
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2. Press `Win+X`, then `I` to open a new PowerShell window
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3. Run `wget
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'https://api.bintray.com/content/basespace/BaseSpaceCLI-EarlyAccess-BIN/latest/\$latest/amd64-windows/bs.exe?bt_package=latest'
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-O $env:LOCALAPPDATA\Microsoft\WindowsApps\bs.exe`
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4. Close PowerShell
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5. Open Cygwin Console and run
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```bash
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BS=$(cygpath "C:\Users\\$USER\AppData\Local\Microsoft\WindowsApps\bs.exe")
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$BS auth
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```
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6. Copy the given link, navigate to it in a browser, and login to Illumina
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Basespace
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7. In Cygwin console now run
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```bash
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git clone https://github.com/MillironX/wphl-bioinformatics.git
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cp wphl-bioinformatics/illumina/dl-fastqs.sh ~
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chmod +x dl-fastqs.sh
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```
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8. Right-click the Windows desktop, and click "New | Shortcut..."
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9. Type `C:\cygwin64\bin\bash.exe` and click Next
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10. Type `Download Illumina Run` or something else memorable and click "Finish"
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11. Right-click the newly created shortcut and click Properties
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12. In the Target textbox, add a space and `--login dl-fastqs.sh` to the
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existing text
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13. Click OK
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## FASTQ Sorters
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These scripts change the file names of the FASTQ files to correspond with the
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well positions during prep phases.
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### Usage
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To be run with Julia.
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```powershell
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julia --project=PATH_TO_ILLUMINA_FOLDER PATH_TO_SORTING_SCRIPT
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```
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In practice, this looks like
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```powershell
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julia --project=C:\Users\MillironX\illumina C:\Users\MillironX\illumina\sort-miseq.jl
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```
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### Installation
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These scripts require [Julia](https://julialang.org).
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1. Download and install Julia
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1. Select "Add Julia to PATH" as an option
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2. All other default options will work
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2. Download the Repo's ZIP file (click green button on upper-right)
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3. Press `Win+R`, type `%USERPROFILE%` and press Enter
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4. Copy the illumina folder from the ZIP file into the newly opened folder
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5. Press `Win+X`, then `I` to open a new PowerShell window
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6. Type `julia --project=$env:USERPROFILE\illumina` and press Enter
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7. Press the `]` key, the prompt should change to say `(illumina) pkg>`
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8. Run `instantiate`
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9. Press the backspace key to return to the `julia>` prompt
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10. Run `exit()`
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11. Close PowerShell
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12. Right-click the Windows desktop, and click "New | Shortcut..."
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13. Type `julia --project=%USERPROFILE%\illumina
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%USERPROFILE%\illumina\sort-miseq.jl` and click Next
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14. Type `Sort MiSeq Run` or something else memorable and click "Finish"
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15. Right-click the Windows desktop, and click "New | Shortcut..."
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16. Type `julia --project=%USERPROFILE%\illumina
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%USERPROFILE%\illumina\sort-nextseq.jl` and click Next
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17. Type `Sort NextSeq Run` or something else memorable and click "Finish"
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