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资源说明：Source tree graph database
[](http://travis-ci.org/OpenTreeOfLife/treemachine) # 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](http://opentreeoflife.org/). 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](http://brew.sh): ``` 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 $(NEO4J_HOME)/plugins ``` ## Usage ### Constructing a DB First, compile the command-line version (see above). Then, to build the DB: ``` java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar ingestsynth newick_tree json_annotations tsv_taxonomy DB_name ``` where: * `newick_tree` is the `labelled_supetree/labelled_supertree.tre` from the synthesis procedure * `json_annotations` is the `annotated_supertree/annotations.json` from the supertree procedure * `tsv_taxonomy` is the `taxonomy.tsv` file from the [Open Tree of Life Taxonomy (OTT)](https://tree.opentreeoflife.org/about/taxonomy-version/) * `DB_name` is the name for the directory that will hold the generated DB (you choose) ### Serving a DB with Neo4j Compile the server plugins (see 'Server plugins, above). Before starting neo4j, you will need to modify file `$(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 ```
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