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!
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 $INSTALL_DIR, will generate a folder named gedi (containing the source code) and a folder named bin (containing the scripts and compiled program files) The second command just created a temporary variable containing the current working directory.
There are two options:
Always call it with its full path (use the bin folder generated above instead of
<BIN-FOLDER>/gedi -e Version
or put this folder into your PATH variable:
export PATH=$PATH:<BIN-FOLDER>
gedi -e Version