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Update README to specify Java 17
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jrobinso committed Jan 26, 2024
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# igv

![Build Status](https://github.com/igvteam/igv/actions/workflows/gradle_test.yml/badge.svg)
![GitHub issues](https://img.shields.io/github/issues/igvteam/igv)
![GitHub closed issues](https://img.shields.io/github/issues-closed/igvteam/igv)
Expand All @@ -8,51 +9,54 @@ Integrative Genomics Viewer - desktop genome visualization tool for Mac, Windows

### 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).
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.
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.
IGV requires **Java 17** to build and run. Later versions of Java should work but we build and test on **Java 17**.

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.
* 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
* 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.
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

* 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/).
* 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.
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).
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
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/)
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/).


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