Sage-Bionetworks / synapser

An R package providing programmatic access to Synapse

synapser

The synapser package provides an interface to Synapse, a collaborative workspace for reproducible data intensive research projects, providing support for:

• integrated presentation of data, code and text
• fine grained access control
• provenance tracking

The synapser package lets you communicate with the Synapse platform to create collaborative data analysis projects and access data using the R programming language. Other Synapse clients exist for Python, Java, and the web browser.

Requirements

• R version 4.1.3 or higher
• Python version 3.8 or higher
• Synapse account

Installation

synapser is available as a ready-built package for Microsoft Windows and Mac OSX. For Linux systems, it is available to install from source. Please also check out our System Dependencies article for instructions on how to install system dependencies on Linux environments.

synapser can be installed or upgraded using the standard install.packages() command, adding the Sage Bionetworks R Archive Network (RAN) to the repository list, e.g.:

install.packages("synapser", repos=c("http://ran.synapse.org", "https://cloud.r-project.org"))

Alternatively, edit your ~/.Rprofile and configure your default repositories:

options(repos=c("http://ran.synapse.org", "https://cloud.r-project.org"))

after which you may run install.packages without specifying the repositories:

install.packages("synapser")

If you have been asked to validate a release candidate, please use:

install.packages("synapser", repos=c("http://staging-ran.synapse.org"))

Under the hood, synapser uses reticulate and the synapsePythonClient, which is why you are required to have an installation of Python if you don't already. See instructions below on installing/upgrading Python below.

Usage

To get started, try logging into Synapse. If you don’t already have a Synapse account, register here:

library(synapser)
synLogin()

Please visit the synapser docs site or view our vignettes for using the synapser package:

browseVignettes(package = "synapser")

Usage Examples

knit2synapse

Knit RMarkdown files to Synapse wikis

syndccutils

Code for managing data coordinating operations (e.g., development of the CSBC/PS-ON Knowledge Portal and individual Center pages) for Sage-supported communities through Synapse.

How to Upgrade Python

On Windows

• Download the Python installer from the Official Website of Python here.

• Install the Downloaded Python Installer

• check Install Python and Check the “Add python.ext to PATH”, then click on the “Install Now” button.

• Verify the Update

  python --version

• Note If it still shows the old version, you may restart your system. Or uninstall the old version from the control panel.

On macOS

• Both python 2x and 3x can stay installed in a MAC. Mac comes with python 2x version. To check the default python version in your MAC, open the terminal and type

  python --version
  python3 --version

• If you don't then go ahead and install it with the installer. Go the the python's official site here.

• Now restart the terminal and check again with both commands python —version

  python3 --version

• Or use to install last version

  brew install python3 && cp /usr/local/bin/python3 /usr/local/bin/python

On Linux

• Add the repository and update

  sudo add-apt-repository ppa:deadsnakes/ppa
  sudo apt-get update

• Update the package list

  apt-get update

• Verify the updated Python packages list

  apt list | grep python3.10

• Install the Python 3.10 package using apt-get

  sudo apt-get install python3.10

• Add Python 3.8 & Python 3.10 to update-alternatives

  sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 1
  sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.10 2

• Update Python 3 for point to Python 3.10

  sudo update-alternatives --config python3

How to Upgrade R

• Verify R version
  • Open RStudio > At the top of the Console you will see session info > The first line tells you which version of R you are using.
  • or write in console >'R.version.string' to print out the R version.
  • go to Tools > Check for Package Updates. If there's an update available for tidyverse, install it.

On Windows

• To update R on Windows, try using the package installer (only for Windows).
• Got to Tools (at the top) > Check for package updates. If tidyverse shows up on the list, select it, then click “Install Updates.”

On Mac

• Go to here.
• Click the link you need to update R pkg
• When the file finishes downloading, double-click to install. You should be able to click “Next” to all dialogs to finish the installation.
• From within RStudio, go to Help > Check for Updates to install newer version of RStudio (if available, optional).
• To update packages, go to Tools > Check for Package Updates. If updates are available, select All (or just tidyverse), and click Install Updates.