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anngvu committed Mar 13, 2024
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21 changes: 15 additions & 6 deletions vignettes/package-installation.Rmd
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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

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### 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



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### Login

```{r, eval=FALSE}
```
library(nfportalutils)
syn_login()
```



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