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NCI Cancer Genomics Cloud Hackathon Tutorials

Workshop tutorial: [html] [R markdown] [R script]

R Package for Seven Bridges Platform

You can also checkout the bioconductor page for more information

Features

  • Complete API R client with user friendly API like

a$project("demo")$file("sample.tz")$delete()

a$project(id = "tengfei/quickstart")$upload("folder_path", metadata = list(platform = "Illumina"))

  • CWL Tool interface, you can directly describe your tool in R, export to JSON/YAML, or add it to your online project. This package defines a complete set of CWL object.

  • Task monitoring hook allow you to add hook function to task status when you monitor a task, for example, when task is finished sent you email or download all files.

  • Cross platform support, if it's cwl compatible platform from Seven Bridges, like Cancer genomics cloud or Seven bridges on google and AWS, you can use it.

  • Authentification management for multiple platforms/users via config file.

Tutorials

Tutorials are listed on bioconductor page

browseVignettes("sevenbridges")

Installation

The package is currently not available in the Bioconductor release branch yet until next Bioc release cycle, please switch to the devel branch by following code to install.

source("http://bioconductor.org/biocLite.R")
useDevel(devel = TRUE)
biocLite("sevenbridges")

Alternatively, you can install the latest development version of the package from GitHub too:

# install.packages("devtools") if devtools was not installed
source("http://bioconductor.org/biocLite.R")
##  useDevel() ## ignore the erro if you cannot use devel
## biocLite("BiocUpgrade") ## don't have to run
library(devtools)
install_github("tengfei/sevenbridges", build_vignettes=TRUE, 
  repos=BiocInstaller::biocinstallRepos(),
  dependencies=TRUE)

If you have trouble with pandoc, either instal it or set build_vignettes = FALSE,

To load the package in R, simply call

library("sevenbridges")

Launch Rstudio Server and Shiny Server with sevenbridges IDE docker container

docker run  -d -p 8787:8787 -p 3838:3838 tengfei/sevenbridges

check out the ip from docker machine if you are on mac os.

docker-machine ip default

In your browser,

http://<url>:8787/ for Rstudio

http://<url>:3838/<username of rstudio>/app_dir for Shiny server

For example, if 192.168.99.100 is what returned, visit http://192.168.99.100:8787/ for Rstudio.

Note: for users of that Rstudio, just create ShinyApps folder under your home folder, then put your apps under that folder, so you can visit http://<url>:3838/<username of rstudio>/<app name> for your shiny apps. For example

In your Rstudio server launched from container, please run

file.copy("/usr/local/lib/R/site-library/shiny/examples/01_hello/", "~/ShinyApps/", recursive = TRUE)

If you are login as username 'rstudio', then visit http://192.168.99.100:3838/rstudio/01_hello you should be able to see the hello example.

© Seven Bridges Genomics 2012 - 2016. Licensed under the MIT license.