phylodb and Algorithms Jars

For this first step, it is necessary to assure that you have Java, Maven and Gradle installed. Notice that Java and Gradle must be compatible. Then, you can follow or the instructions from 1, or from 2 or from 3, that simply use the jars previously generated for testing phyloDB in localhost.

1. Using an IDE - IntelliJ

1. Open IntelliJ and select get from VCS (version control system). Then, fill with the phyloDB repository address and with the local directory.

2. Then, build the respective jars:
   1. Jar for the algorithms project. To do that it is needed to execute the command mvn package -Dmaven.test.skip=true on the phyloDB-master/algorithms project folder.
   2. Jar for the phyloDB project. Make sure that your gradle and java are compatible. To build the respective jar of this project, it is needed to execute the command bootJar on the phyloDB-master/phylodb project folder.

(i)

(ii)

This will produce a jar at phyloDB/build/libs directory. The phylodb project contains the api. Note: for this example to work, the key spring.data.neo4j.uri, in application.properties file , must have the value bolt://database_host:7687, where database_host must be replaced for the host of the database.

2. OR using command line

1. Download the source code of phyloDB. This will produce the file phyloDB-master.zip.
2. Extract the previous file.
3. Then, build the respective jars:
   1. Jar for the algorithms project. To do that it is needed to execute the command mvn package -Dmaven.test.skip=true on the phyloDB-master/algorithms project folder. The produced jar will be phyloDB-master/algorithms/target directory. The algorithms project contains the user defined procedures that shall be used by the Neo4j database. With this step, the provided algorithms are packaged in a jar file.
   2. Jar for the phyloDB project. Make sure that your gradle and java are compatible. To build the respective jar of this project, it is needed to execute the command chmod 700 gradlew and then the command gradlew bootJar on the phyloDB-master/phylodb project folder. Note, in mac the command is ./gradlew bootJar. This will produce a jar at phyloDB/build/libs directory. The phylodb project contains the api. Note:. for this example to work, the key spring.data.neo4j.uri, in application.properties file , must have the value bolt://database_host:7687, where database_host must be replaced for the host of the database.

3. OR Using the jars previous generated for testing in localhost

Alternatively, you can use these jars from release https://github.com/phyloviz/phyloDB/releases/tag/v1.0.0 where the database host is localhost. In this, case, for the next steps, it is necessary to:

1. Download the source code of phyloDB.
2. Extract the previous file.
3. Put the algorithms-1.0jar on the phyloDB-master/algorithms/target project folder.
4. Put the phylodb-1-0-0.jaron the the phyloDB-master/phylodb project folder.

You can then proceed to Step 2