# igv
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Integrative Genomics Viewer - desktop genome visualization tool for Mac, Windows, and Linux.

### Building

These instructions are meant for developers interested in working on the IGV code.  For normal use,
we recommend the pre-built releases available at [http://software.broadinstitute.org/software/igv/download](http://software.broadinstitute.org/software/igv/download).

Builds are executed from the IGV project directory.  Files will be created in the 'build' subdirectory.

IGV requires **Java 11** to build and run.   Later versions of Java should work but we build and test  on **Java 11**. Previous (versions =< 2.6.3) running on Java8 have been deprecated.

NOTE: If on a Windows platform use ```./gradlew.bat'``` in the instructions below

#### Folder structure and build targets

The IGV bundles ship with embedded JREs from AdoptOpenJDK.

* Install Gradle for your platform.  See https://gradle.org/ for details.

* Use ```./gradlew createDist``` to build a distribution directory (found in ```build/IGV-dist```) containing 
  the igv.jar and its required runtime third-party dependencies as well as helper scripts for launching.

    * Launch IGV with `igv.sh` or `igv_hidpi.sh` on Linux, `igv.command` on Mac, and `igv.bat` on Windows.

    * To run igvtools from the command line use the script `igvtools` on Linux and Mac, or igvtools.bat
      on Windows.  See the instructions in igvtools_readme.txt in that directory.

    * The launcher scripts expect this folder structure in order to run IGV.
  
* Use ```./gradlew test``` to run the test suite.  See 'src/test/README.txt' for more information about running
  the tests.
  
* See this [README](https://raw.githubusercontent.com/igvteam/igv/master/scripts/readme.txt) for tips about using the IGV launcher scripts.

* This dashboard describes [project structure and dependencies](https://sourcespy.com/github/igvteamigv/). 


Note that Gradle creates a number of other subdirectories in 'build'.  These can be safely ignored.

#### Amazon Web Services support

Public data files hosted in Amazon S3 buckets can be loaded into IGV using [https endpoints](https://docs.aws.amazon.com/AmazonS3/latest/dev/UsingBucket.html).  

Authenticated access using s3:// urls is supported by either (1) enabling OAuth access with Cognito using the UMCCR 
contributed AWS configuration option, or (2) setting AWS credentials and region information as described 
[here]( https://docs.aws.amazon.com/sdk-for-java/v1/developer-guide/credentials.html) and 
[here](https://docs.aws.amazon.com/sdk-for-java/v1/developer-guide/java-dg-region-selection.html).

For more details on using Cognito for OAuth access, see the [UMCCR documentation on the backend](https://umccr.org/blog/igv-amazon-backend-setup/) 
and [frontend for a provisioning URL step by step guide](https://umccr.org/blog/igv-amazon-frontend-setup/).


 
