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Overview

sevenbridges-r is an R/Bioconductor package that provides an interface for the Seven Bridges Platform and Cancer Genomics Cloud public APIs.

The Seven Bridges Platform is a cloud-based environment for conducting bioinformatic analyses. It is a central hub for teams to store, analyze, and jointly interpret their bioinformatic data. The Platform co-locates analysis workflows 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 Genome 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 own data to analyze alongside TCGA using predefined analytical workflows or your own tools.

Table of Contents

Installation

Bioconductor - Release Version

This installation is recommended for most users as it is the most stable. The current release of Bioconductor is version 3.5, and it works with R version 3.4.0. Users of older R and Bioconductor versions should upgrade to take advantage of new features.

If you do not want to update R, please install the sevenbridges package directly from GitHub by following the instructions below.

Check R version

First, check which version of R you are using with the following:

R.version.string

If you are not running the latest release version of R, install it by the following these instructions. If you are using RStudio, close and restart RStudio after installing R. RStudio will detect the new installation.

Install the package

Install the sevenbridges package as shown below:

source("https://bioconductor.org/biocLite.R")
biocLite("sevenbridges")

Bioconductor - Development Version

If you are developing tools in the devel branch or if you are a user who uses the development version for R and Bioconductor, install the package from the bioconductor devel branch. You need to install R-devel first by following the directions in "Using the 'Devel' Version of Bioconductor". After upgrading R, this method of installation is harder. To try the latest features, please install directly from GitHub as next shown below:

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

To load the package in R, simply call

library("sevenbridges")

Latest Development Version

You can always install the latest development version of the sevenbridges package from GitHub. We push to the Bioconductor branch (release/devel) regularly.

If devtools was not installed

Installing the sevenbridges package requires you have the devtools package. If you do not have devtools, install it from CRAN.

install.packages("devtools")

You may got an error and need system dependecies for curl and ssl. For example, you probably need to do the following first in order to install devtools and in order to build vignettes since you need pandoc under Ubuntu.

apt-get update
apt-get install libcurl4-gnutls-dev libssl-dev pandoc pandoc-citeproc

If devtools is already installed

Install latest version of sevenbridges from GitHub with the following:

source("https://bioconductor.org/biocLite.R")
biocLite("readr")

devtools::install_github(
    "sbg/sevenbridges-r",
    repos = BiocInstaller::biocinstallRepos(),
    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.

Features

The sevenbridges package includes the following features:

Flexible Authentication Methods

  • Multiple authentication methods support.

Direct authentication:

# direct authentication
a <- Auth(token = "your_token", platform = "cgc")
# or use base url
a <- Auth(token = "your_token", url = "https://cgc-api.sbgenomics.com/v2")

Authentication via system environment variables:

sbg_set_env(token = "your_token", url = "https://cgc-api.sbgenomics.com/v2")
a <- Auth(from = "env")

Authentication via a user configuration file, collect and manage your credentials for multiple accounts across various Seven Bridges environments:

a <- Auth(from = "file", profile_name = "aws-us-tengfei")

Please check vignette("api", package = "sevenbridges") for technical details about all available authentication methods.

Complete API R Client

  • 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 = "tengfei/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"))

Task Monitoring

  • 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:
setTaskHook("completed", function() {
    tsk$download("~/Downloads")
})
tsk$monitor()

Batch Tasks Support

  • 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)))

Cross Environment Support

Common Workflow Language Tool Interface

  • 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:
library("readr")
fd <- fileDef(name = "runif.R", content = 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"))

# output CWL JSON
rbx$toJSON(pretty = TRUE)
# output CWL YAML
rbx$toYAML()

Utilities for Tool and Flow

  • Utilities for Tool and Flow, for example
# converting a SBG CWL JSON file
library("sevenbridges")
t1 <- system.file("extdata/app", "tool_star.json", package = "sevenbridges")
# convert json file into a Tool object
t1 <- convert_app(t1)
# shows all input matrix
t1$input_matrix()

Tutorials

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
<a name="ide"/>IDE container: Rstudio and Shiny server and more HTML Source
Browse data on the Cancer Genomics Cloud via the Data Explorer, a SPARQL query, <br />or the Datasets API HTML Source

IDE Docker Image

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.

docker-machine ip default

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 02_text at ~/ShinyApps/02_text/.

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 rstudio, visit 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 /srv/shiny-server/.

FAQ

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?<br />
    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?<br />
    A: We support draft 2 and are making progress on supporting draft 3.

  • Q: Is there a Python binding for the API?<br />
    A: Yes, the official Python client is here. Recipes and tutorials using the Python bindings are here.

  • Q: Why do I get warning messages when I use the API R client?<br />
    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.<br />
    A: Please try to use the latest package on GitHub or update installed Bioconductor packages. This usually includes the most recent bug fixes.

Events

Time Event Location
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)<br />[HTML] [R Markdown Source] Seven Bridges Genomics, Inc., Boston, MA

Contribute

Please file bug reports/feature requests on the issue page, or create pull requests here.

Contributors should read the Seven Bridges Notice to Contributors and sign the Seven Bridges Contributor Agreement before submitting a pull request.

Copyright

© 2017 Seven Bridges Genomics, Inc. All rights reserved.

This project is licensed under the terms of the Apache License 2.0.

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