Install and run bioLQM
BioLQM is freely available without guarantees, under theand licenses.
In the following, we describe the installation methods.
1 - Use the released jar file
BioLQM requires the, 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).
Some features (notably for the identification of trapspaces) further rely on theavailable in your execution path.
To install bioLQM, download the jar file associated to the latest. 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 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
2 - Conda package and docker image
BioLQM is included in the. In a working conda environment (we recommend the use of , 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.
3 - Building from source
Building bioLQM from source further requires a Java Compiler (JDK) and the.
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>