The synapser
package provides an interface to Synapse, a collaborative workspace for reproducible data intensive research projects, providing support for:
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.
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:
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.
To get started, try logging into Synapse. If you don’t already have a Synapse account, register here:
Please visit the synapser
docs site or view our vignettes for using the synapser
package:
browseVignettes(package = "synapser")
Knit RMarkdown files to Synapse wikis
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.
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
Note
If it still shows the old version, you may restart your system. Or uninstall the old version from the control panel.
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
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
Or
use to install last version
or
write in console >‘R.version.string’ to print out the R version.