How to install a phylogenetic tree pattern matching service

First of all, download the whole package in your working directory:

git clone https://github.com/SouthGreenPlatform/rap-green.git

Step 1: java pattern matching daemon installation and configuration

The pattern matching daemon is a Java process that load the phylogenetic tree collection in the RAM, and interact with the tree pattern editor using a client-server protocol, taking in charge the combinatory part of the method. So, the daemon should be installed in a server with enough RAM (count 3-5 Go for 1,000,000 terminal genes). The daemon server should be visible from the web server that will host the www facilites, and a logical port should be opened.

• Compile the RapGreen java package (mostly tested in Java 1.8, but compatible with newer of older versions):

cd rap-green

javac rapgreen/*.java

• Prepare your files, one must contain the phylogenetic tree collection, and one must contain the species tree labeled with internal and terminal taxa.
  • The phylogenetic tree collection contains one tree per line, composed with the family identifier (any unique label) and the tree in NHX format. NHX zone must hold a :S= for the species at the leaves, and a D=Y/N for duplication/speciation nodes (duplication, yes or no). An example is provided in: rap-green/example_files/phylo_tree_collection_example.nwk

Step 2: installation of the tree pattern editor

• Download