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Updated README.md
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IgorRodchenkov committed May 18, 2024
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Expand Up @@ -46,15 +46,17 @@ $ paxtools help
* Older BioPAX [snapshots](http://www.biopax.org/m2repo/snapshots/) and [releases](http://www.biopax.org/m2repo/releases/) Maven2 repository
* [Downloads](http://www.biopax.org/downloads/paxtools/)

More information about Paxtools can be found in [the publication](http://dx.plos.org/10.1371/journal.pcbi.1003194), [wiki archive](http://www.biopax.org/mediawiki/index.php/Paxtools), and [BioPAX forum](https://groups.google.com/d/msg/biopax-discuss/zwtwDG23T1E/Vu1OK7iXBQAJ).
More information about Paxtools can be found in [the publication](http://dx.plos.org/10.1371/journal.pcbi.1003194),
[wiki archive](http://www.biopax.org/mediawiki/index.php/Paxtools), and
[BioPAX forum](https://groups.google.com/d/msg/biopax-discuss/zwtwDG23T1E/Vu1OK7iXBQAJ).

(_TODO_: move the Paxtools description here and deprecate that wiki soon.)

## Build

To build or use with a modern JDK (>11), e.g., OpenJDK-19, additional java options are required:
```bash
export _JAVA_OPTIONS="--add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED"
export JDK_JAVA_OPTIONS="--add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED"
```
(can also add to the java command args)

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