diff --git a/vignettes/package-installation.Rmd b/vignettes/package-installation.Rmd index e9923f2b..b674dbe3 100644 --- a/vignettes/package-installation.Rmd +++ b/vignettes/package-installation.Rmd @@ -19,10 +19,10 @@ knitr::opts_chunk$set( THIS VERSION: This is the recommended installation for the [current release](https://github.com/nf-osi/nfportalutils/releases/tag/v0.9500-presynapser) of `nfportalutils` **that does not depend on `synapser`**. - There *will* be a **newer version of `nfportalutils` with `synapser`** (i.e. see [this issue](https://github.com/nf-osi/nfportalutils/issues/94) on the roadmap), and instructions will be accordingly revised when the refactor is completed. -Make sure you are in a new R session (in RStudio, go to `Session > Restart R` if necessary). +Make sure you are in a new R session (in RStudio, go to `Session > Restart R` if necessary). +The trickiest part of the installation and package usage, for most R users, will be the Python interop. ### Windows @@ -133,7 +133,17 @@ SYNAPSE_AUTH_TOKEN=xxx_your_token_here_xxx ### MacOS -TODO +#### Outside R + +- If Python is not already installed, obtain Python3 via `brew` following suggested method here: https://docs.python-guide.org/starting/install3/osx/#doing-it-right. +- Install `synapseclient` following instructions at https://pypi.org/project/synapseclient/4.0.0/. + +### Linux (Ubuntu) + +#### Outside R +- Python is already included, so just need https://pypi.org/project/synapseclient/4.0.0/. + +#### With R @@ -146,11 +156,10 @@ Without a token, you are logged in as "Anonymous" and functionality will be limi ### Login -```{r, eval=FALSE} - +``` library(nfportalutils) syn_login() - ``` +