Install and run bioLQM

BioLQM is freely available without guarantees, under the LGPL v3+ and CeCILL-C 2.1 licenses.

In the following, we describe the installation methods.

1 - Use the released jar file

BioLQM requires the Java 8 Runtime, available for Linux, Windows and Mac systems (older Macs come with an unsupported version of Java, which could complicate the installation of Java 8). Use the following command to see you java version (it should be 1.8.x). 

java -version

Some features (notably for the identification of trapspaces) further rely on the clingo ASP solver available in your execution path.

To install bioLQM, download the jar file associated to the latest release. You can then running bioLQM on the command-line with the java environment. The following command will display a help message, see the documentation of the command-line interface to start using it. 

java -jar bioLQM-#version.jar

The JAVA virtual machine provide many options of its own, for large models, bioLQM could mostly benefit from extending the amount of memory available, with the -Xmx option. For example, one can launch bioLQM with 1000MB of memory using java -Xmm1000M -jar bioLQM-#version.jar. For more details, see the java tools documentation

2 - Conda package and docker image

BioLQM is included in the conda package for GINsim. In a working conda environment (we recommend the use of MiniConda 3, the following command will to install GINsim, BioLQM, and their dependencies. A *bioLQM* command should then be available in your environment. These packages are tested on Linux (x64), but should also work on Mac OSX and Windows platforms. 

conda install -c colomoto ginsim

These conda packages are used to build a consistent and reproducible environment integrating several software tools for the analysis of qualitative models, as described in https://colomoto.github.io/colomoto-docker/.

3 - Building from source

Building bioLQM from source further requires a Java Compiler (JDK) and the Maven build tool.

git clone https://github.com/colomoto/bioLQM.git
cd bioLQM
mvn package

Maven downloads all requirements and generates the target folder containing the jar file along with a lib folder for dependencies. These dependencies are bundled with the release jar.

4 - Maven

To integrate BioLQM in your Java software using Maven, put the following in your pom.xml file:

      <repositories>
        <repository>
           <id>ginsim_snapshot</id>
           <name>GINsim snapshot repository</name>
           <snapshots><enabled>true</enabled></snapshots>
           <releases><enabled>false</enabled></releases>
           <url>http://ginsim.org/maven/snapshot</url>
        </repository>
        <repository>
           <id>ginsim_stable</id>
           <snapshots><enabled>false</enabled></snapshots>
           <releases><enabled>true</enabled></releases>
           <name>GINsim deps</name>
           <url>http://ginsim.org/maven/stable</url>
        </repository>
      </repositories>

      <dependencies>
        <dependency>
          <groupId>org.colomoto</groupId>
          <artifactId>bioLQM</artifactId>
          <version>0.6-SNAPSHOT</version>
        </dependency>
      </dependencies>