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https://github.com/igvteam/igv
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
https://github.com/igvteam/igv
Last synced: 3 days ago
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Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
- Host: GitHub
- URL: https://github.com/igvteam/igv
- Owner: igvteam
- License: mit
- Created: 2012-02-11T17:30:30.000Z (almost 13 years ago)
- Default Branch: main
- Last Pushed: 2025-01-16T17:25:36.000Z (10 days ago)
- Last Synced: 2025-01-17T00:07:42.679Z (10 days ago)
- Language: Java
- Homepage: https://igv.org
- Size: 428 MB
- Stars: 653
- Watchers: 48
- Forks: 387
- Open Issues: 165
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: license.txt
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
- Awesome-Bioinformatics - IGV js - Java-based browser. Fast, efficient, scalable visualization tool for genomics data and annotations. Handles a large variety of formats. [ [paper-2019](https://pubmed.ncbi.nlm.nih.gov/31099383) | [web](https://software.broadinstitute.org/software/igv) ] (Visualization / Genome Browsers / Gene Diagrams)
README
# igv
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 21** to build and run. Later versions of Java should work but we build and test on **Java 21**.
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/).