API for calling interactively the GMQL Engine from R/Bioconductor
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.
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.
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
Edit the .bash_profile
and add the JAVA_HOME
environment variable:
export JAVA_HOME = <java_path>
export PATH=$PATH
Since on macOS Catalina the default shell is Zsh we need to edit or create the .zsh file:
Edit the .zsh
and add the JAVA_HOME
environment variable:
export JAVA_HOME = <java_path>
export PATH=$PATH
At the end, in both cases, edit the /etc/paths
and add:
$JAVA_HOME/bin
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")
Create environment variable JAVA_HOME
:
JAVA_HOME
variable the jdk pathBe 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:
https://github.com/steveloughran/winutils/tree/master/hadoop-2.8.1
and download the winutil-hadoop2.8.1C:\Program Files\hadoop\bin
), using a path you wishor
C:\Program Files\hadoop\bin
), using a path you wishAdd the following code to your website.
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