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Install the Standalone Distribution

The standalone distribution is a self-contained bundle of the TASSEL JAR, its libraries, and helper launch scripts. It is ideal for running TASSEL from the command line, on a server, or inside an analysis pipeline.

Unlike the native GUI installers, the standalone distribution does not bundle a Java runtime, so you need Java installed yourself.

Prerequisites

  • Java 21 (JDK or JRE) on your PATH. Verify with:

    java -version

  • Perl to use the .pl launch scripts (pre-installed on macOS and most Linux distributions). On Windows, use the provided .bat scripts instead.

  • (Optional, recommended) OpenBLAS for faster native matrix operations.

Download

Grab the latest standalone archive from the Download page (select Standalone), or directly:

A .zip archive is also published on the releases page for each version.

Extract

The archive unpacks into a single version-named folder, so you can keep several versions side by side without them overwriting each other.

tar -xzf tassel-5-standalone-v5.2.98.tar.gz
cd tassel-5-standalone-v5.2.98

Extract the .zip with File Explorer (right-click → Extract All), then open a Command Prompt in the tassel-5-standalone-v5.2.98 folder that contains sTASSEL.jar. File Explorer proposes a destination folder named after the archive, so accepting the default nests the distribution one level deeper; the .bat scripts must be run from the folder holding the JAR.

Archives from 5.2.97 and earlier

Older archives have no enclosing folder: they unpack their contents straight into the current directory. Create a directory and extract from inside it, or pass tar -xzf <archive> -C <directory>.

Run

The distribution ships two entry points:

  • start_tassel — launches the graphical interface.
  • run_pipeline — runs the command-line pipeline.
# Launch the GUI
./start_tassel.pl

# Run a pipeline (example: print the help/usage)
./run_pipeline.pl

:: Launch the GUI
start_tassel.bat

:: Run a pipeline
run_pipeline.bat

Allocating memory

The launch scripts accept a maximum heap size. For large datasets, increase it, for example to 20 GB:

./run_pipeline.pl -Xmx20g ...

Next steps