sevenbridges-r is an R/Bioconductor package that provides an interface for the Seven Bridges Platform (US, EU, China), Cancer Genomics Cloud, Cavatica, and DataSTAGE Powered by Seven Bridges public APIs.
The Seven Bridges Platform is a cloud-based environment for conducting bioinformatics analysis. It is a central hub for teams to store, analyze, and jointly interpret their bioinformatic data. The Platform co-locates analysis pipelines alongside the largest genomic datasets to optimize processing, allocating storage, and compute resources on demand.
The Cancer Genomics Cloud (CGC), powered by Seven Bridges, is also a cloud-based computation environment. It was built as one of three pilot systems funded by the National Cancer Institute to explore the paradigm of colocalizing massive genomics datasets, like The Cancer Genomics Atlas (TCGA), alongside secure and scalable computational resources to analyze them. The CGC makes more than a petabyte of multi-dimensional data available immediately to authorized researchers. You can add your data to analyze alongside TCGA using predefined analytical workflows or your own tools.
Cavatica, powered by Seven Bridges, is a data analysis and sharing platform designed to accelerate discovery in a scalable, cloud-based compute environment where data, results, and workflows are shared among the world’s research community. Cavatica is built in collaboration with the Children Hospital of Philadelphia and it is focused on pediatric data.
First, check the version of R you are using with the following command (in R):
If you are not running the latest release version of R, install or upgrade with these instructions. If you are using RStudio, restart RStudio after installing R. RStudio will detect the new installation.
This is recommended for most users as it is the most stable version.
You can install the package from the
release branch on Bioconductor using
If you are developing tools under the
devel branch or use the development version of R and Bioconductor, install the package from the Bioconductor
devel branch. You probably also want to install R-devel first by following the directions in “Using the ‘Devel’ Version of Bioconductor”.
To install the
sevenbridges package from the
devel branch, use
To try the latest features, please install the package directly from GitHub. We push to the Bioconductor branch (
sevenbridges package from GitHub requires you have the
devtools package. If you do not have
devtools, install it from CRAN first.
You may get an error for missing system dependecies such as curl and ssl. You probably need to do the following first in order to install
devtools and to build vignettes since you need
pandoc under Ubuntu.
devtools is installed, install the latest version of
sevenbridges from GitHub:
install.packages("BiocManager") devtools::install_github( "sbg/sevenbridges-r", repos = BiocManager::repositories(), build_vignettes = TRUE, dependencies = TRUE )
If you have trouble with
pandoc and do not want to install it, set
build_vignettes = FALSE to avoid building the vignettes.
sevenbridges package includes the following features:
Multiple authentication methods support.
sbg_set_env(token = "your_token", url = "https://cgc-api.sbgenomics.com/v2") a <- Auth(from = "env")
a <- Auth(from = "file", profile_name = "aws-us-username")
vignette("api", package = "sevenbridges") for technical details about all available authentication methods.
A complete API R client with a user-friendly, object-oriented API with printing and support operations for API requests relating to users, billing, projects, files, apps, and tasks. Short examples are also included, as shown below:
# Get a project by pattern-matching its name p <- a$project("demo") # Get a project by its id p <- a$project(id = "username/demo") # Delete files from a project p$file("sample.tz")$delete() # Upload fies from a folder to a project and include file metadata p$upload("folder_path", metadata = list(platform = "Illumina"))
A task monitoring hook which allows you to add a hook function to specific task statuses as you monitor a task. For example, you can opt to receive an email when the task is completed or specify to download all files produced by the task, as shown below:
Batch tasks by metadata and by item.
# Batch by item (tsk <- p$task_add( name = "RNA DE report new batch 2", description = "RNA DE analysis report", app = rna.app$id, batch = batch(input = "bamfiles"), inputs = list( bamfiles = bamfiles.in, design = design.in, gtffile = gtf.in ) )) # Batch by metadata. Note that input files must # have relevant metadata fields specified. (tsk <- p$task_add( name = "RNA DE report new batch 3", description = "RNA DE analysis report", app = rna.app$id, batch = batch( input = "fastq", c("metadata.sample_id", "metadata.library_id") ), inputs = list( bamfiles = bamfiles.in, design = design.in, gtffile = gtf.in ) ))
A Common Workflow Language (CWL) Tool interface to directly describe your tool in R, export it to JSON or YAML, or add it to your online project. This package defines a complete set of CWL object, so you can describe tools as follows:
fd <- fileDef(name = "runif.R", content = readr::read_file(fl)) rbx <- Tool( id = "runif", label = "runif", hints = requirements( docker(pull = "rocker/r-base"), cpu(1), mem(2000) ), requirements = requirements(fd), baseCommand = "Rscript runif.R", stdout = "output.txt", inputs = list( input(id = "number", type = "integer", position = 1), input(id = "min", type = "float", position = 2), input(id = "max", type = "float", position = 3) ), outputs = output(id = "random", glob = "output.txt") ) # Print CWL JSON rbx$toJSON(pretty = TRUE) # Print CWL YAML rbx$toYAML()
Flow, for example
We maintain 3 different sets of documentation: the sevenbridges-r GitHub repository (latest and most up-to-date), Bioconductor release channel, and Bioconductor development channel. Below, only the GitHub version is linked to provide the latest documentation. For the other versions, please visit Bioconductor Release version or Bioconductor Development version. The tutorials below are re-generated regularly as we update the package on GitHub.
|Tutorial Title||HTML||Rmd Source|
|Complete Reference for the API R Client||HTML||Source|
|Use R on the Cancer Genomics Cloud||HTML||Source|
|Create a Docker Container and use Command Line Interface for R||HTML||Source|
|Describe and execute Common Workflow Language (CWL) Tools and Workflows in R||HTML||Source|
|IDE container: Rstudio and Shiny server and more||HTML||Source|
|Browse data on the Cancer Genomics Cloud via the Data Explorer, a SPARQL query,
or the Datasets API
In the tutorial for IDE container above, we built a Docker container locally from which we can launch RStudio and Shiny. To launch RStudio and Shiny Server with the Seven Bridges IDE Docker container, do the following:
docker run -d -p 8787:8787 -p 3838:3838 --name rstudio_shiny_server sevenbridges/sevenbridges-r
To mount a file system, you need to use
--privileged with fuse.
docker run --privileged -d -p 8787:8787 -p 3838:3838 --name rstudio_shiny_server sevenbridges/sevenbridges-r
Check out the IP from Docker Machine if you are on a Mac OS.
In your browser, you can see where the RStudio server is located from the path
http://<url>:8787/. For example, if 192.168.99.100 is returned, visit
http://192.168.99.100:8787/ for Rstudio.
For the Shiny server, each app__ is hosted at
http://<url>:3838/users/<username of rstudio>/<app_dir> for the Shiny server. For example, an app called
01_hello owned by user
rstudio (a default user) has the path
http://<url>:3838/users/rstudio/01_hello/. To develop your Shiny apps as an Rstudio user, you can login your RStudio server and create a folder in your home folder called
~/ShinyApps. There, you can develop shiny apps in that folder. For example, you can create an app called
Log into your RStudio at
http://<url>:8787. Then, try to copy an app to your home folder, as follows:
dir.create("~/ShinyApps") file.copy( "/usr/local/lib/R/site-library/shiny/examples/01_hello/", "~/ShinyApps/", recursive = TRUE )
If you are logged in as user
http://192.168.99.100:3838/rstudio/01_hello. You should be able to see the “hello” example.
Note: Generic Shiny apps can also be hosted at
http://<url>:3838/ or, for a particular app, at
http://<url>:3838/<app_dir>. Inside the Docker container, it’s hosted under
The best place to ask questions about the
sevenbridges package is the mailing list.
Q: Does this package support Seven Bridges’ API v1 which was not CWL compatible?
A: No. This package only supports API v2 +. For API v1, please check out the sbgr package. Note that API v1 and associated legacy project types will be deprecated eventually.
Q: Which version of the Common Workflow Language (CWL) is supported?
A: We support draft 2 and are making progress on supporting draft 3.
Q: Why do I get warning messages when I use the API R client?
A: The warning only exists in Rstudio and is potentially a bug in Rstudio. To ignore, it use
options(warn = -1)
Q: I still have problems despite dismissing the messages.
A: Please try to use the latest package on GitHub or update installed Bioconductor packages. This usually includes the most recent bug fixes.
|Jan 12, 2017||Genomics in the Cloud - Boston Bioconductor Meetup (talk) [slides]||Dana-Farber Cancer Institute, Boston, MA|
|Sep 12 - 14, 2016||Probabilistic Modeling in Genomics (poster)||University of Oxford, Oxford, UK|
|May 27 - 29, 2016||The 9th China-R Conference (talk)||Renmin University of China, Beijng, China|
|Jun 27 - 30, 2016||The R User Conference 2016 (talk)||Stanford University, Stanford, CA|
|Jun 24 - 26, 2016||BioC 2016: Where Software and Biology Connect (workshop)||Stanford University, Stanford, CA|
|Apr 1 - 3, 2016||
NCI Cancer Genomics Cloud Hackathon (tutorial)
[HTML] [R Markdown Source]
|Seven Bridges Genomics, Inc., Boston, MA|
© 2018 Seven Bridges Genomics, Inc. All rights reserved.
This project is licensed under the terms of the Apache License 2.0.