README.md

In RGMQL: GenoMetric Query Language for R/Bioconductor

RGMQL

API for calling interactively the GMQL Engine from R-Bioconductor

RGMQL on Bioconductor

Requirements

The library requires the following: R version 3.4.2 or higher Java version 1.8 or higher * The JAVA_HOME enviroment variable set

It is recommended the use ot the latest version of RStudio.

OSX Settings

before Catalina

Edit the .bash_profile and add the JAVA_HOME environment variable:

export JAVA_HOME = <java_path>

export PATH=$PATH

after Catalina

Since on macOS Catalina the default shell is Zsh we need to edit or create the .zsh file:

Edit the .zsh and add the JAVA_HOME environment variable:

export JAVA_HOME = <java_path>

export PATH=$PATH

At the end, in both cases, edit the /etc/paths and add:

$JAVA_HOME/bin

Windows Settings

Create environment variable JAVA_HOME:

• Right click on This PC.
• click on Advanced system settings
• go to Advanced tab an click on evnironment variables
• create a JAVA_HOME variable the jdk path

Errors

Be aware that during a local-processing execution an error message

Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, 
: org.apache.spark.SparkException: Job aborted due to stage failure: 
Task 0 in stage 7.0 failed 1 times, most recent failure: 
Lost task 0.0 in stage 7.0 (TID 59, localhost, executor driver): 
java.io.IOException: (null) entry in command string: null chmod 0644

may arise.

This happens because some Hadoop binary files are missing in Windows 64Bits. In this case we need to:

• Open DownGit
• Paste the url https://github.com/steveloughran/winutils/tree/master/hadoop-2.8.1 and download the winutil-hadoop2.8.1
• Create a directory (for example at C:\Program Files\hadoop\bin. Use a path you wish
• Copy the files from the repository folder hadoop-2.8.1 into the folder earlier created.
• Create environment variable HADOOP_HOME with value equal to the folder path you copied the binaries.

or

• Go to https://github.com/steveloughran/winutils, download the repository
• Create a directory (for example at C:\Program Files\hadoop\bin. Use a path you wish
• Copy the files from the repository folder hadoop-2.8.1 into the folder earlier created.
• Create environment variable HADOOP_HOME with value equal to the folder path you copied the binaries.

RGMQL documentation built on Nov. 8, 2020, 5:59 p.m.