AnnoTALE

AnnoTALE is a command-line toolkit for analysing transcription activator-like effector (TALE) proteins.

Prerequisites

• Java 8

• Apache Maven 3.6+

• Maven downloads standard plugins from Maven Central: ensure network access for the first build.

Repository layout

• src/main/java -- Java sources under the annotale package
• src/main/resources -- runtime assets (TALE HMMs, help text, icons)

Building the CLI jar

AnnoTALE depends on Jstacs. You need to build and install the dependency into your local maven repository by running mvn install in the Jstacs repo root. Then build the AnnoTALE jar in the AnnoTALE repo root via:

mvn package

The build produces target/AnnoTALEcli-1.4.1.jar. Verify it with:

java -jar target/AnnoTALEcli-1.4.1.jar --help

Legacy Ant build

The original ant task still lives at src/AnnoTALEcli.xml. It rebuilds the same shaded jar into dist/AnnoTALEcli-1.4.1.jar.

Licensing information

AnnoTALE is free software: you can redistribute it and/or modify under the terms of the GNU General Public License version 3 or (at your option) any later version as published by the Free Software Foundation.