Improve install instructions and remove workbench refs (#221)

* Move install instructions to overview, include Vice app use

* Remove getting started and workbench info from README

* Remove all references to workbench in tutorials

Author: KristinaRiemer

README.md

@@ -1,59 +1,39 @@
 [![Travis-CI Build Status](https://travis-ci.org/terraref/tutorials.svg?branch=master)](https://travis-ci.org/terraref/tutorials)
 
-# Tutorials
+# TERRA REF Documentation
 
+## Overview
 
-## An introduction to the use of TERRA REF data and software
+In this repository is an extensive set of materials for how to use TERRA REF data and software. 
+The best place to start is the [TERRA REF tutorials website](https://terraref.github.io/tutorials/). 
+We used [bookdown](https://bookdown.org/) to create the website, and relevant files include _[bookdown.yml](https://github.com/terraref/tutorials/blob/master/_bookdown.yml), [index.Rmd](https://github.com/terraref/tutorials/blob/master/index.Rmd), and all of the [vignettes](https://github.com/terraref/tutorials/tree/master/vignettes). 
 
-This repository provides a set of tutorials that are divided by data types and use cases. 
+Tutorials on the website come from the more extensive tutorials in the [traits](https://github.com/terraref/tutorials/tree/master/traits), [sensors](https://github.com/terraref/tutorials/tree/master/sensors), and [plantcv](https://github.com/terraref/tutorials/tree/master/plantcv) folders. 
+Notes from walkthroughs of TERRA REF data use are in [videos](https://github.com/terraref/tutorials/tree/master/videos). 
 
-In the repository, you will find three folders that contain examples of how to access data:
+These are intended to cover diverse use cases, and you will find information about accessing data from web interfaces but the primary focus is on accessing data using R, Python, SQL, and REST APIs. These are intended to provide quick-start introductions to access data along with computing environments required for further exploration. They are not intended to teach analyses, although some illustrative visualizations and statistical models are provided.
 
-* traits
-* sensors
-* plantCV
+This is a work in progress for an open source community that welcomes contributions in many forms. Please feel welcome to ask questions, provide suggestions, or share analyses that may be of interest to others.
 
-Within each folder there are both R markdown and Jupyter notebooks. These describe different approaches to accessing data. These are intended to cover diverse use cases, and you will find information about accessing data from web interfaces but the primary focus is on accessing data using R, Python, SQL, and REST APIs. These are intended to provide quick-start introductions to access data along with computing environments required for further exploration. They are not intended to teach analyses, although some illustrative visualizations and statistical models are provided.
+## How to contribute
 
-This is a work in progress, and an open source community that welcomes contributions in many forms. Please feel welcome to ask questions, provide suggestions or share analyses that may be of interest to others.
+We welcome suggestions and edits from all users. 
+Feel free to [create a GitHub issue](https://github.com/terraref/tutorials/issues) detailing possible improvements. 
 
+If you would like to make changes yourself, fork this repository, make changes on a branch, and submit a pull request. 
+We are happy to help with this process. 
 
-## Getting Started
-
-### Requirements
-
-All of the tutorials have been designed to work in the cloud and can be accessed using a web browser. Therefore, the _only technical requirements_ are:
-* Web browser
-* Internet connection
-
-In addition, you will need to:
-* Sign up as as a TERRA REF [Beta User by filling out this application](http://terraref.org/beta).
-* Sign up for an account on the [TERRA REF Workbench](https://www.workbench.terraref.org), and wait for approval.
-
-### Using the Workbench
-
-The Workbench uses the National Data Service Labs Workbench (NDS Labs Workbench) software. The Workbench is a cloud analysis environment that minimizes and standardizes the software requirements so users can get started quickly. It also provides access to large files and databases that would otherwise be slow and impractical for users to download and store. 
-
-Although we provide a few pre-configured computing environments, Workbench is designed to support any Docker container - that is, anything you can install on a linux computer can be used in the workbench - for an idea of what is possible, see the large number of options on [Docker Hub](https://hub.docker.com/explore/).
-
-**To get started**, follow the [Workbench Quick Start](https://htmlpreview.github.io/?https://github.com/terraref/tutorials/blob/master/workbench/ndslabs_workbench_intro.html).
-
-This will walk you through the process of getting started with the first tutorials on how to access data.
-
-
-## To generate this documentation locally
-
-If you would like to contribute to this documentation you can preview your 
-changes by running the following command:
+There are two ways to preview your changes as you make them. 
+The first is by running the following on the command line from within the forked repository folder:
 
 ```bash
 Rscript -e 'bookdown::render_book("index.Rmd")'
 ```
 
 The output will be in the `docs` folder.
 
-There is also a Dockerfile for convenience. It requires installing Docker on 
-your computer:
+The second way to preview changes is using the Docker container. 
+This requires installing Docker on your computer:
 
 - [Docker for Mac](https://download.docker.com/mac/stable/Docker.dmg)
 - [Docker for Windows](https://download.docker.com/win/stable/Docker%20for%20Windows%20Installer.exe) 
@@ -73,4 +53,4 @@ docker run --rm -p 3000:3000 --name tutorial-preview terraref-tutorials:local
 This will generate the documentation and start a local web server to preview
 your changes. Open the preview URL in your browser: <http://localhost:3000/>
 
-Run `docker kill tutorial-preview` to kill the web server container. 
+Run `docker kill tutorial-preview` to kill the web server container. 

index.Rmd

@@ -35,7 +35,53 @@ At a minimum, you should have:
 * Software:
     + Software requirements vary with the tutorials, and may be complex
 
-### User Accounts and permission to access TERRA REF data {#user-accounts}
+### Installation instructions {#installation-instructions}
+
+**Option 1** The recommended and easier option is to use our [VICE](https://learning.cyverse.org/projects/vice/en/latest/getting_started/about.html) app on [CyVerse](https://cyverse.org/)'s [Discovery Environment](https://de.cyverse.org/de/) platform. All necessary programs and libraries are installed and accessed using RStudio. You'll need a CyVerse account; follow instructions below to set up. 
+
+Launching TERRA REF app on VICE: 
+
+1. Google "Cyverse" and click link to website
+2. Select Products tab
+3. Under "Discovery Environment", select Launch button
+4. Hit "Log in with your CyVerse ID" button
+5. Log in with CyVerse credentials (username and password)
+6. Select "Apps", type in "terra", select "TERRA REF Rstudio 3.6.0", and "Use App"
+7. Click "Launch Analysis", hit Analysis button, and select arrow button in Analyses window
+8. Wait patiently
+9. Sign into RStudio using username: rstudio and password: rstudio1
+
+Reopen running TERRA REF instance: 
+
+1. Google "Cyverse" and click link to website
+2. Select Products tab
+3. Under "Discovery Environment", select Launch button
+4. Hit "Log in with your CyVerse ID" button
+5. Log in with CyVerse credentials (username and password)
+6. Open Analyses window and hit arrow button to open up RStudio
+
+**Option 2** Everything necessary can be installed locally instead of using the VICE app. 
+You will need to [install R](https://www.r-project.org/) and a handful of R packages. 
+
+All of the packages except `traits` are available on CRAN and can be installed using the `install.packages` function:
+
+```r
+install.packages('tidyverse', 'jsonlite', 'knitr', 'lubridate', 'raster', 'sf')
+```
+
+Although `traits` is also on CRAN, you need to download the TERRA REF version from GitHub to handle larger datasets: 
+
+```r
+install.packages('devtools')
+devtools::install_github('terraref/traits')
+```
+You will additionally need to [install Python](https://www.python.org/downloads/) and the `terrautils` library, as below: 
+
+```sh
+pip install terrautils
+```
+
+### User accounts and permission to access TERRA REF data {#user-accounts}
 
 The first few chapters in the 'vignettes' section use publicly available sample data sets.
 Subsequent sections are also written to use publicly available data sets, but some of the examples require data that requires users to sign up.

sensors/01-meteorological-data.Rmd

@@ -206,7 +206,7 @@ This higher resolution weather data can be used for VNIR calibration, for exampl
 
 #### Download data
 
-Here we will download the files using the Clowder API, but note that if you have access to the filesystem (on www.workbench.terraref.org or globus, you can directly access the data in the `sites/ua-mac/Level_1/EnvironmentLogger`. Folder
+Here we will download the files using the Clowder API, but note that if you have access to the filesystem on Globus, you can directly access the data in the `sites/ua-mac/Level_1/EnvironmentLogger` folder. 
 
 ```{r met-setup2}
 knitr::opts_chunk$set(eval = FALSE)

sensors/06-list-datasets-by-plot.Rmd

@@ -8,7 +8,7 @@ the API key that will be used in this tutorial.
 
 The terrautils python package has a new `products` module that aids in connecting
 plot boundaries stored within betydb with the file-based data products available
-from the workbench or Globus.
+from Globus.
 
 * if are using Rstudio and want to run the Python code chunks, the R package "reticulate" is required
 * use `pip3 install terrautils` to install the terrautils Python library

traits/07-betydb-sql-access.Rmd

@@ -2,11 +2,6 @@
 
 will be derived from https://github.com/pi4-uiuc/2017-bootcamp/blob/master/content/post/2017-05-30-databases-and-sql.Rmd#with
 
-## On workbench
-
-On the TERRA REF Workbench, you have access to the database. These connections will only work if you are on the workbench.
-
-
 ## Using PostgresSQL Studio
 
 

vignettes/00-introduction.Rmd

@@ -6,36 +6,15 @@
 These vignettes provide a **quick start** tutorial - they quickly show you how to access different types of data in the TERRA Reference datasets and perform ‘hello world’ tasks with them. 
 
 The vignettes currently include examples of:
+
 * trait data
 * weather data
 * image data
 * combining trait, weather, and image data in a single analysis
 
-In order to make these vignettes as easy to use as possible, we are using a subset of the full dataset that is is available without an account or password. Specifically, we have made data from thirty two plots in each of the two seasons available. 
+In order to make these vignettes as easy to use as possible, we are using a subset of the full dataset that is available without an account or password. Specifically, we have made data from thirty two plots in each of the two seasons available. 
 
 Although we want to make these data broadly available, the remainder of the dataset requires an account to use so we can keep track of who and how many people are using it, and can contact users with their provided email addresses. 
-Information for getting a beta user account is available in the section on [User Accounts](#user-accounts).
-
-
-## Prerequisites
-
-### R
-
-In order to use the vignettes, you will need to have R installed along with the extra packages that are used. 
-All of the packages except 'trait' are available on CRAN and can be installed using the `install.packages` function:
-
-```r
-install.packages('tidyverse', 'jsonlite', 'knitr', 'lubridate', 'raster', 'sf')
-```
-
-Although 'traits' is also on CRAN, you need to download the TERRA REF version from GitHub to handle larger datasets: 
-
-```r
-install.packages('devtools')
-devtools::install_github('terraref/traits')
-```
-### Python
+Information for getting a beta user account is available in the section on [User accounts](#user-accounts).
 
-```sh
-pip install terrautils
-```
+See [Installation instructions](#installation-instructions) in the Overview.