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README.md

Build Status

treemachine-LITE

Description

treemachine-LITE is a pared-down version of the original treemachine which was used to generate synthetic phylogenetic trees for the Open Tree of Life project. Synthetic analyses are now performed by other tools. The role of treemachine-LITE is simply to construct a neo4j database and serve such trees.

Installing dependencies

treemachine-LITE is managed by Maven v.3 (including the dependencies). In order to compile and build treemachine-LITE, it is easiest to let Maven v.3 do the hard work.

maven On Linux you can install Maven v.3 with:

sudo apt-get install maven

On Mac OS, Maven v.3 can be installed with Homebrew:

brew install maven

jade and ot-base Once Maven v.3 is installed, the treemachine-LITE dependencies themselves can be installed with:

mvn_install_dependencies.sh

neo4j The DB constructed by treemachine-lite is meant to be served by neo4j. We are currently using neo4j-community-v1.9.5. To obtain and decompress neo4j:

$ curl http://files.opentreeoflife.org/neo4j/neo4j-community-1.9.5-unix.tar.gz > neo4j-community-1.9.5.tar.gz
$ tar xzf neo4j-community-1.9.5.tar.gz

Alternately, there is a make target for neo4j:

make neo4j

You can move the neo4j directory wherever you like.

Compiling treemachine-LITE

NOTE: The script for compiling the server plugins will delete any command-line jar in the target directory (and the opposite is true - compiling the command-line jar will delete the server plugins from the target directory). You can rebuild either just by running those scripts again.

Command-line version

To compile the command-line version (which you can then use to build a database):

sh mvn_cmdline.sh

This creates treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar in the target directory (and deletes the server plugin jar if it existed).

Server plugins

To compile the server plugins for interacting with the graph over REST calls:

sh mvn_serverplugins.sh

This creates treemachine-neo4j-plugins-0.0.1-SNAPSHOT.jar in the target directory (and deletes the command-line jar if it existed). Then, copy the .jar file into the neo4j plugins directory:

cp -p target/treemachine-neo4j-plugins-0.0.1-SNAPSHOT.jar $(NEO4J_HOME)/plugins

Usage

Constructing a DB

First, compile the command-line version (see above). Then, to build the DB:

java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar ingestsynth newick_tree json_annotations tsv_taxonomy DB_name

where:

  • newick_tree is the labelled_supetree/labelled_supertree.tre from the synthesis procedure
  • json_annotations is the annotated_supertree/annotations.json from the supertree procedure
  • tsv_taxonomy is the taxonomy.tsv file from the Open Tree of Life Taxonomy (OTT)
  • DB_name is the name for the directory that will hold the generated DB (you choose)

Serving a DB with Neo4j

Compile the server plugins (see 'Server plugins, above). Before starting neo4j, you will need to modify file $(NEO4J_HOME)/conf/neo4j-server.properties. Put the full path of the DB directory constructed by treemachine-LITE as the value for the org.neo4j.server.database.location setting.

After you have loaded content into your db, you can run the neo4j http server with the command :

neo4j-community-1.9.5/bin/neo4j start

If you add the neo4j-community-1.9.5/bin directory to your path, you can just say neo4j start.

Running the tests

To make sure everything is running ok, run the web service tests:

cd ws-tests
./run_tests.sh host:apihost=http://localhost:7474 host:translate=true