igv.js-flask

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Example project for integrating igv.js and flask

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# IMPORTANT

This repository is an example of an integration of igv.js with a Flask server.   It is not an active development project and not maintained.   Our efforts are focused on the [igv.js component itself](https://github.com/igvteam/igv.js).  For an example of a complete website integrating igv.js for use with any web server, including Flask,  see [igv-webapp](https://github.com/igvteam/igv-webapp).

## Notes on sample data

The sample project includes test data in "static/data/public".   The bedgraph and bigwig files in that directory contain data on chr1 (only).  The "gsst1.bam" file contains data for the gstt1 locus, specifically ```chr22:24,374,133-24,386,311```.

## Installation
You can install all required packages including Flask using [pip](https://pip.pypa.io/en/stable/).
```sh
pip install -r requirements.txt
```
## Running the app
To run the app using the simple builtin server, you can use the provided run file:
```sh
python run.py
```

Now that the server is running, go to (http://localhost:5000) to use IGV.
To view one of the example tracks, click on it in the box in the upper left corner.

Alternatively, you can set the environment variable FLASK_APP to igvjs.py and use 'flask run':
```sh
export FLASK_APP=igvjs.py
flask run
```
Note: With this method, you can use the command-line options for flask run. For
example, use the -p option to set port number. Use --host=0.0.0.0 to make the
server externally visible (eg. flask run -p 8659 --host=0.0.0.0).

## Additional Flask Blueprints

Additional Flask Blueprints are defined in the project for the following:

### UCSC Blueprint

The UCSC genome database may be directly accessed with this blueprint.

The mysql connection needs to be installed for this blueprint to work:

```
pip install mysql-connector==2.1.7
```
Restarting the application and going to (http://localhost:5000/ucsc) links up with the UCSC database.

A full set of parameters (db, table, chr, start, end) needs to be provided as GET parameters, e.g. (http://localhost:5000/ucsc?db=hg38&table=knownGene&chr=chrX&start=15560138&end=15602945). See the[UCSC Table Browser](https://genome.ucsc.edu/cgi-bin/hgTables) for inspiration on what parameter values to use.

### Alignment Blueprint

The [pysam module needs to be installed](https://pysam.readthedocs.io/en/latest/installation.html) for this Blueprint to work (this may be a non-trivial installation on some machines).

Restarting the application and going to (http://localhost:5000/alignments) links up with the UCSC database.

### Configuration

Configuration options can be set in _config.py in the root directory.

Currently supported options are:  
USES_OAUTH - whether or not data is protected using OAuth  
ALLOWED_EMAILS - the filename containing the list of allowed emails when using OAuth  
PUBLIC_DIR - path to directory of public data when using OAuth (eg. /static/data/public)

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