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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.

Most of the tools and methods developed in the group are part of, or a plugin to Gedi (e.g. LFC, PRICE, GRAND-SLAM, Peptide-PRISM).

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.

How to run

There are two options:

  • Always call it with its full path (use the bin folder generated above instead of ):
<BIN-FOLDER>/gedi -e Version
export PATH=$PATH:<BIN-FOLDER>
gedi -e Version