Welcome to the GEDI

Gedi is a software platform for working with genomic data such as sequencing reads, sequences, per-base numeric values or annotations written in Java.

Gedi is developed in the erhard-lab.

For documentation, see here!

News

• 7.2.2024: We now use Maven instead of Ant as our build system, and do not support Java 8 anymore

Installation

Prerequisites

• Java 11 or higher
• Maven for the build script

Installing Gedi

Follow these steps for installing Gedi:

INSTALL_DIR="$HOME/gedi"  # change this to any folder you like to install gedi to
mkdir -p $INSTALL_DIR
cd $INSTALL_DIR

git clone git@github.com:erhard-lab/gedi.git

mkdir bin
cd bin

mvn -f $INSTALL_DIR/gedi/Gedi package 

This will create the folder defined in $INSTALL_DIR, and inside of $INSTALL_DIR, will generate a folder named gedi (containing the source code) and a folder named bin (containing the scripts and compiled program files). The second command just created a temporary variable containing the current working directory.

The bin directory should contain the following files

• bamlist2cit
• gedi
• Gedi-VERSION.jar (VERSION is the current version of gedi)
• gedi.jar (softlink)
• lib (subfolder)

Important: Pay attention that the folder where you execute 'mvn ...' is empty!

How to run

There are two options:

• Always call it with its full path (use the full path to the bin folder generated above instead of ):

<BIN-FOLDER>/gedi -e Version

• or put this folder into your PATH variable:

export PATH=$PATH:<BIN-FOLDER>
gedi -e Version