manics / romero-gateway

OMERO R Gateway

OMERO R Gateway

R wrapper around the OMERO Java Gateway, to enable access to OMERO via R using rJava

Prerequisites

• R
• Java
• rJava (Installation)
• devtools
• Apache Maven (recommended)
• Git (recommended)

Build/Install the romero.gateway R package

• Install/Setup the software mentioned above

Automated

• Download and run install.R script (requires Maven and Git):

  Rscript install.R
  

  You can specify a particular branch or version to build/install or perform a local build of the cloned repository. Run Rscript install.R --help to see more details.

Manual

• Download this repository:
  • Using Git: git clone https://github.com/ome/rOMERO-gateway.git
  • Alternative: Download as Zip and extract.
• cd into the rOMERO-gateway directory
• Download the dependencies
  • Using Maven: Run mvn install
  • Alternative: Create inst/java directory. Download OMERO.insight client. Extract the zip file. Copy all files within libs directory into the previously created rOMERO/inst/java directory
• Launch the R console
• Load devtools library library(devtools)
• Build the package devtools::build()
• Install the romero.gateway package into your local R repository

  install.packages([PATH TO romero.gateway_x.y.z.tar.gz], repos = NULL, type="source")
  

Usage

• Like any other R package load the package library(romero.gateway)
• Try some examples from the examples directory

Testing

• Install testthat
• Spin up an OMERO server to test against
• Adjust and run test-data script to populate the test server
• Adjust setup.csv to match your test server setup (mostly omero.host etc; the various ids should be ok if you used the test-data script to populate the server)
• Run devtools::test()

Remarks

Installing rJava

Before installing the rJava package you probably have to set up Java for R first:

# as root
export $JAVA_HOME=[path to JDK/JRE]
R CMD javareconf

Additional dependencies

In order to build/install some necessary R packages, additional system libraries may have to be installed first. E.g. the R packages httr and xml2 need the development libraries for curl and xml2, so for example on a Debian system you most likely have to install libcurl4-dev and libxml2-dev first.