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You will find here tutorials describing use cases of RAPPAS as well as comments on the different analysis options it provides. All tutorials are valid for a UNIX or MAC operating system. RAPPAS can be installed on Windows systems but you will need to adapt the following commands accordingly.
- RAPPAS compilation requires a clean JDK 1.8 javac compiler installation. Java >=1.8 is a compulsory requirement as some operations are based on Lambda expressions.
- Apache Ant is used to facilitate the compilation.
If not already done, please install the OpenJDK libraries of the proprietary Oracle JDK 1.8.
Using OpenJDK 1.8:
#install packages
sudo apt-get update
sudo apt-get install openjdk-8-jdk
#update relevant symlinks to make v1.8 default
sudo update-java-alternatives --set java-1.8.0-openjdk-amd64
Using the proprietary Oracle JDK 1.8:
#install packages
sudo add-apt-repository ppa:webupd8team/java
sudo apt-get update
sudo apt-get install oracle-java8-installer
#update relevant symlinks to make v1.8 default
sudo apt-get install oracle-java8-set-default
Installation of Apache Ant:
sudo apt-get install ant
If everything went fine, the command java -version should return lines similar to:
java version "1.8.0_161" <<--- the version must be > 1.8.x
Java(TM) SE Runtime Environment (build 1.8.0_161-b12)
Java HotSpot(TM) 64-Bit Server VM (build 25.161-b12, mixed mode)
If not already done, please install the OpenJDK libraries of the proprietary Oracle JDK 1.8.
Download the JDK from the Oracle JDK 8 webpage.
Unpack the jdk by running the file jdk-8uxxx-macosx-x64.dmg.
Your JDK is installed. Note that you may have to explicitely export the JDK with the command:
export JAVA_HOME=/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home
To avoid to reproduced this step, just add the line in your bash profile.
If everything went fine, the command java -v should return lines similar to:
java version "1.8.0_161" <<--- the version must be > 1.8.x
Java(TM) SE Runtime Environment (build 1.8.0_161-b12)
Java HotSpot(TM) 64-Bit Server VM (build 25.161-b12, mixed mode)
This tutorial is an analogue to the tutorial provided on this page.
- Open a terminal and create a working directory.
mkdir RAPPAS_tutorial_1 cd RAPPAS_tutorial_1 - Download RAPPAS and the tutorial dataset
git clone -b master https://github.com/blinard-BIOINFO/RAPPAS.git - Move into the tutorials 1 directory