RGMQL

API for calling interactively the GMQL Engine from R/Bioconductor

RGMQL on Bioconductor

About

RGMQL is a R/Bioconductor package conceived to provide a set of specialized functions to extract, combine, process and compare omics datasets and their metadata from different and differently localized sources. RGMQL is built over the GenoMetric Query Language (GMQL) data management and computational engine, and can leverage its open curated repository as well as its cloud-based resources, with the possibility of outsourcing computational tasks to GMQL remote services. Furthermore, it overcomes the limits of the GMQL declarative syntax, by guaranteeing a procedural approach in dealing with omics data within the R/Bioconductor environment. But mostly, it provides full interoperability with other packages of the R/Bioconductor framework and extensibility over the most used genomic data structures and processing functions.

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.

Structure

RGMQL/
|-- Example of workflows/
|   |-- EXAMPLES.Rproj
|   |-- use_case_1.Rmd
|   |-- use_case_2.Rmd
|   |-- use_case_3.Rmd
|   |-- use_case_1.html
|   |-- use_case_2.html
|   |-- use_case_3.html
|   |-- ....
|-- R/
|-- inst/
|   |-- example/
|   |-- NEWS
|-- man/
|-- vignettes/
|   |-- RGMQL-vignette.R
|   |-- RGMQL-vignette.Rmd
|   |-- RGMQL-vignette.html
|   |-- american-medical-association-no-et-al.csl
|   |-- bibliography.bib
|   |-- ....
|-- DESCRIPTION
|-- NAMESPACE
|-- README.md

• Examples of workflows/ folder containing various use cases
• R/ folder containing all the script files
• inst/ folder containing all files that should be copied into the installed R package folder
• inst/example folder containing the datasets and other files in order to run correctly all the test
• inst/NEWS file report the feature/changes/bugfix for each version
• man/ folder containing R documentation files
• vignettes/ folder containing all the files used to generate correctly the vignette
• vignettes/RGMQL-vignette.R long-form guide to your package
• vignettes/RGMQL-vignette.Rmd vignettes in markup language
• vignettes/RGMQL-vignette.html vignettes in html
• vignettes/bibliography.bib the bibliographic file with list of references used in vignettes
• vignettes/american-medical-association-no-et-al.csl the citation style language used in vignettes
• DESCRIPTION this file stores important/mandatory metadata about RGMQL package
• NAMESPACE this file makes your packages self-contained, ensuring that other packages do not interfere with your code, that your code does not interfere with other packages, and that your package works regardless of the environment in which it is running
• README the current file

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

Errors

Be aware that using a too recent Java version (e.g., the Java version 17) on macOS Mojave currently gives errors in running RGMQL. Conversely, macOS Big Sur runs smoothly RGMQL also with the last Java version 17.

To overcome this issue, we suggest macOS Mojave users to configure rJava to use an older version, like the Java version 11, by running the following command:

sudo R CMD javareconf JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-11.0.13.jdk/Contents/Home

Also, check that Java in use is actually version 11 and, then, check the rJava version used in R, by running:

library(rJava)

.jinit()

.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")

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 the following error message may arise:

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

This happens because some Hadoop binary files are missing in Windows 64 bits. In this case you 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 folder (for example at C:\Program Files\hadoop\bin), using a path you wish
• Copy the files from the repository folder hadoop-2.8.1 into the folder earlier created
• Create the environment variable HADOOP_HOME with value equal to the folder path where you copied the binaries.

or

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