IGV Genome Browser App

Author

Jenny L. Smith

1 IGV

Use VSCode to remote connect to the PromethION instrument by remote-ssh in vscode. Then launch a locally hosted IGV webserver.

Please ask Marika Guercio or Francesca Benini for the remote connection details.

Important

Set-up your environment by running these commands:

export PROJ_DIR=$HOME/Documents/quintarelli_c && source $PROJ_DIR/.bash_profile

2 To launch the application

On the commandline enter the following:

IGV_WEBAPP=$PROJ_DIR/opt/igv-webapp.3.0.7
npx http-server -t30 -c-1 -a localhost $IGV_WEBAPP

Select the PORTS tab from the IGV terminal pane.
Right click (cmd+click on MacOS) on the blue hyperlink localhost:XXXX
Select Open in Browser from the pull-down menu
VCF files and processed WGS data is included in a track called WGS Nanopore T-ALL in the pull down-menu

3 IGV Documentation and Resources

Short video tutorials
IGV Application User Guide

The web application uses the same user guide as the desktop application

IGV Web application documentation

Mainly for deployment docs

---
title: "IGV Genome Browser App"
format: 
  html:
    code-fold: false
    code-tools: true
    toc: true
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author: "Jenny L. Smith"
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## IGV 

Use VSCode to remote connect to the PromethION instrument by `remote-ssh` in vscode. Then launch a locally hosted IGV webserver.

Please ask Marika Guercio or Francesca Benini for the remote connection details. 

::: {.callout-important}

0. Set-up your environment by running these commands:


`export PROJ_DIR=$HOME/Documents/quintarelli_c && source $PROJ_DIR/.bash_profile`

:::

## To launch the application

1. On the commandline enter the following:

```
IGV_WEBAPP=$PROJ_DIR/opt/igv-webapp.3.0.7
npx http-server -t30 -c-1 -a localhost $IGV_WEBAPP
```

2. Select the `PORTS` tab from the IGV terminal pane.

3. Right click (cmd+click on MacOS) on the blue hyperlink `localhost:XXXX`

4. Select `Open in Browser` from the pull-down menu

5. VCF files and processed WGS data is included in a track called `WGS Nanopore T-ALL` in the pull down-menu


## IGV Documentation and Resources 

1. Short video [tutorials](https://www.youtube.com/@IGVtutorials)

2. IGV Application [User Guide](https://igv.org/doc/desktop/#UserGuide/loading_data/)
  - The web application uses the same user guide as the desktop application

3. IGV [Web application documentation](https://igv.org/doc/webapp/)
  - Mainly for deployment docs