knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "README-" )
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", "http://cran.fhcrc.org"))
Alternatively, edit your ~/.Rprofile and configure your default repositories:
options(repos=c("http://ran.synapse.org", "http://cran.fhcrc.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.
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")
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.
{bash eval=F}
python --version
Note
If it still shows the old version, you may restart your system. Or uninstall the old version from the control panel.{bash eval=F}
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
{bash eval=F}
python3 --version
Or
use to install last version
{bash eval=F}
brew install python3 && cp /usr/local/bin/python3 /usr/local/bin/python
{bash eval=F}
sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt-get update
{bash eval=F}
apt-get update
Verify the updated Python packages list
{bash eval=F}
apt list | grep python3.10
Install the Python 3.10 package using apt-get
{bash eval=F}
sudo apt-get install python3.10
Add Python 3.8 & Python 3.10 to update-alternatives
{bash eval=F}
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
{bash eval=F}
sudo update-alternatives --config python3
or
write in console >'R.version.string' to print out the R version.Add the following code to your website.
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