Resources Workshop

The two tutorials can be found here:

• Vignette resources demo
• Vignette resources examples

In order to reproduce the two vignettes follow the instructions described in the next sections

Quick Start

For those in hurry:

install.packages(c("readr", "dplyr", "ssh", "resourcer", "DSOpal", "ggrepel"))
install.packages("dsBaseClient", repos = c("https://cran.obiba.org"))
devtools::install_github("isglobal-brge/dsOmicsClient")

Some dependencies can be needed:

install.packages(c("fields","metafor","ggplot2","gridExtra",
                   "data.table", "ggrepel"))

And probably Rtools.

For the others or if you encounter issues, see instructions that follows.

Prerequisites

The resourcer has quite some suggested dependencies. These are only suggestions, meaning that it will depend on the kind of resource that will be accessed at runtime. See the resourcer's Install section for the detail of the dependencies.

For the need of this workshop, only the following R packages are needed: readr, dplyr, ssh, DSOpal, dsBaseClient (Installing dsOmicsClient is optional)

Tidy files:

• readr: Read Rectangular Text Data
• dplyr: A Grammar of Data Manipulation

Remote computation server:

• ssh: Secure Shell (SSH) Client for R

We also need to install those packages to illustrate how to make use of the resources in DataSHIELD

• DSOpal: DataSHIELD Implementation for Opal
• dsBaseClient: DataSHIELD Client Functions
• dsOmicsClient: DataSHIELD client site Omics association functions

In a R console, install these R packages using the commands:

install.packages(c("readr", "dplyr", "ssh"))
install.packages(c("resourcer", "DSOpal"))
install.packages("dsBaseClient", repos = c("https://cran.obiba.org"))
devtools::install_github("isglobal-brge/dsOmicsClient")

Some dependencies can be needed:

install.packages(c("fields","metafor","ggplot2","gridExtra","data.table",
                  "ggrepel"))

1. R environment

For a friendly R environment and being able to run the proposed examples, Rstudio is highly recommended.

Recommended readings from the DataSHIELD's wiki:

• Introduction to R and the R tutorial
• Become familiar with R Studio and basic concepts of R

2. Install system dependencies

R packages often depend on system libraries or other software external to R. These dependencies are not automatically installed.

Ubuntu

# curl requirements:
sudo apt-get install libcurl4-openssl-dev libssl-dev

# openssl requirements:
sudo apt-get install libssl-dev

# ssh requirements:
sudo apt-get install libssh2-1-dev libssh-dev

Conda

# curl requirements:
conda install -c anaconda libcurl

# openssl requirements:
conda install -c conda-forge openssl

# ssh requirements:
conda install -c conda-forge libssh2

# git requirements:
conda install -c conda-forge libgit2

Windows

Additional libraries are not needed.

3. Try it yourself

Try the R code in the R folder.