13-rocker.knit

class: title-slide
count: false

.title[
  # 13 - Rocker
]
.subtitle[
  ## Open Science Tools
]

.author[
  ### Claudio Zandonella & Davide Massidda
]

.institute[

]

---
class: center, middle, inverse
# Step XII: Rocker

---
# Rocker

{{content}}
]
]

- `r-ver` with Base-R
- `rstudio` adds RStudio
- `tidyverse` adds tidyverse and devtools packages
- `verse` adds tex and publishing-related packages

---
# Rocker

.pull-left-30[
.move-down-80[
<img src="images/13-rocker/rocker-logo.png" width="80%" style="display: block; margin: auto;" />
.font-14[
https://www.rocker-project.org/
]
]
]
.pull-right-70[
.move-down-80[
.code-size-12[
```bash
$ docker run --rm -p 8787:8787 -e PASSWORD=my-pw rocker/rstudio:4.1.0
```
]
]

.move-down-50[
.li-small[
{{content}}
]
]
]

- `--rm` (optional)
- `-p 8787:8787` map the port to access RStudio Server
- `-e PASSWORD=my-pw` password for login
  - default username is **`rstudio`**
  - disable authentication `-e DISABLE_AUTH=true`
- `4.1.0` version tag

---

# Rocker

.move-down-50[
.code-size-12[

```bash
Unable to find image 'rocker/rstudio:4.1.0' locally
4.1.0: Pulling from rocker/rstudio
7b1a6ab2e44d: Pull complete 
34cb923ed704: Pull complete 
f2f213d01c8c: Downloading [=======================>         ]  200.7MB/295.8MB
7c05c07f0160: Download complete 
f72cf49d9462: Download complete 
6abf17a5ebed: Downloading [===========================>     ]  171.7MB/218.4MB
9a11ac2d5af1: Download complete 
```
]
]

.move-down-30[
.center[
{{content}}
]
]
]

[http://localhost:8787/](http://localhost:8787/)

---

# Rocker

.pull-left-30[
.move-down-80[
<img src="images/13-rocker/rocker-logo.png" width="80%" style="display: block; margin: auto;" />
.font-14[
https://www.rocker-project.org/
]
]
]
.pull-right-70[
<img src="images/13-rocker/RStudio-Server-login.png" width="100%" style="display: block; margin: auto;" />
]

---

# Rocker

.pull-left-30[
.move-down-80[
<img src="images/13-rocker/rocker-logo.png" width="80%" style="display: block; margin: auto;" />
.font-14[
https://www.rocker-project.org/
]
]
]
.pull-right-70[
<img src="images/13-rocker/RStudio-Server-interface.png" width="100%" style="display: block; margin: auto;" />
]

---

# Rocker Data Storage

.pull-left-40[
#### Upload/Export

<img src="images/13-rocker/RStudio-Server-export.png" width="65%" style="display: block; margin: auto;" />
]
.pull-right-60[
.code-size-14[
{{content}}
]
]

--
#### Bind Mounts

```bash
-v /Users/<user-name>/my-project/:/home/rstudio/my-project/
```

---

# Rocker Data Storage

.pull-left-40[
#### Upload/Export

<img src="images/13-rocker/RStudio-Server-export.png" width="65%" style="display: block; margin: auto;" />
]
.pull-right-60[
.code-size-14[
#### Bind Mounts

```bash
-v /Users/<user-name>/my-project/:/home/rstudio/my-project/
```
.li-small[
- Mounting bind mounts at the runtime automatically assign ownerships to the default users (`rstudio`)
]

{{content}}
]
]

#### Volumes

```bash
-v My-volume:/home/rstudio/my-volume/
```

---

# Rocker Data Storage

.pull-left-40[
#### Upload/Export

<img src="images/13-rocker/RStudio-Server-export.png" width="65%" style="display: block; margin: auto;" />
]
.pull-right-60[
.code-size-14[
#### Bind Mounts

```bash
-v /Users/<user-name>/my-project/:/home/rstudio/my-project/
```
.li-small[
- Mounting bind mounts at the runtime automatically assign ownerships to the default users (`rstudio`)
]

#### Volumes

```bash
-v My-volume:/home/rstudio/my-volume/
```

.code-small[
```bash
#----    Dockerfile    ----#
# Base image
FROM rocker/rstudio:4.1.0

# Create folder and change owner (user:group)
RUN mkdir /home/rstudio/My-project \
      && chown -R rstudio:rstudio /home/rstudio/my-project

# Define volume
VOLUME /home/rstudio/my-project
```
]
]
]

---
## Custom `Dockerfile`

<br>

--
.pull-left-50[
#### Install Dependencies

.code-size-12[
```bash
#----    Dockerfile    ----#
# Base image
FROM rocker/rstudio:4.1.0

# Install external dependencies
RUN apt-get update \
    && apt-get install -y curl

# Install R packages
RUN R -e "install.packages('trackdown')"
```
]
]
.pull-right-50[
.code-size-12[
{{content}}
]
]

#### Run an R script

```bash
#----    Dockerfile    ----#
...

# Install R packages
COPY my-install.R /my-install.R
RUN Rscript my-install.R
```

---
# Rocker Worklow

- **After the Development**

---
# Rocker Worklow

- **After the Development**

- Complete the analysis
  - Create container
  - Re-run the analysis
  
--

- **During the Development**

---
# Rocker Worklow

- **After the Development**

- Complete the analysis
  - Create container
  - Re-run the analysis

- **During the Development**

- Create container
  - Develop from within the container

---
# After the Development

]
]
.pull-right-70[

]

---
# After the Development

]
]
.pull-right-70[
.code-size-12[
{{content}}
]
]

--
#### Define Container

```bash
#----    Dockerfile    ----
FROM rocker/rstudio:4.1.2

# Copy project files
COPY . /home/rstudio/my-project

# Change ownership
RUN chown -R rstudio:rstudio /home/rstudio/
```

---
# After the Development

.code-size-12[
```bash
#----    Dockerfile    ----
FROM rocker/rstudio:4.1.2

# Copy project files
COPY . /home/rstudio/my-project

# Change ownership
RUN chown -R rstudio:rstudio /home/rstudio/
```
]

.move-down-80[
.li-small[
- `.dockerignore` exclude results and not required files
]
]
]

---
# After the Development

---
# After the Development

.pull-left-30[
.code-size-12[
```
My-project/
  |-- .gitignore
  |-- .Rprofile
  |-- _targets.yaml
  |-- DESCRIPTION
  |-- Dockerfile
  |-- my-project.Rproj
  |-- README
  |-- renv.lock
  |-- .git/
  |-- analysis/
  |   |-- _taregts/
  |   |-- targets-analysis.R
  |   |-- targets-workflow.R
  |-- data/
  |   |-- raw-data.csv
  |-- documents/
  |   |-- _targets.yaml
  |   |-- report.Rmd
  |-- R/
  |   |-- my-functions.R
  |   |-- targets-utils.R
  |-- renv/
```
]
]
.pull-right-70[
#### Instructions (continue)
.code-size-14[
.li-size-14[
> - Open the R project by double-clicking the file `my-project/my-project.Rproj` file you can find in the project. A new R-studio session will open.
> - Run `renv::restore()` to install the project’s dependencies (have a coffee, it takes some time).
> - Run `targets::tar_make()` to run the analysis using `targets`. (Note that this will properly work because we defined targets script and store locations in the `_targets.yaml` file).
> - To compile the report, open `documents/report.Rmd` and compile the file
>     clicking the `Knitr` button  (or run `rmarkdown::render(input = 'documents/report.Rmd')`).
]
]
]

---
# After the Development

.code-size-12[
```bash
#----    Dockerfile    ----
FROM rocker/rstudio:4.1.2

# Copy project files
COPY . /home/rstudio/my-project

# Change ownership
RUN chown -R rstudio:rstudio /home/rstudio/
```
]
]

---
# After the Development

.code-size-12[
```bash
#----    Dockerfile    ----
FROM rocker/rstudio:4.1.2

# Copy project files
COPY . /home/rstudio/my-project

*# Install renv
*ENV RENV_VERSION 0.15.1
*ENV RENV_PATHS_CACHE /home/rstudio/.cache/R/renv
*RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
*RUN R -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"

*# Install packages
*WORKDIR /home/rstudio/my-project
*RUN R -e "renv::restore()"

# Change ownership
RUN chown -R rstudio:rstudio /home/rstudio/
```
]
]

---
# After the Development

.code-size-12[
```bash
#----    Dockerfile    ----
FROM rocker/rstudio:4.1.2

# Copy project files
COPY . /home/rstudio/my-project

# Install renv
ENV RENV_VERSION 0.15.1
ENV RENV_PATHS_CACHE /home/rstudio/.cache/R/renv
RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
RUN R -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"

# Install packages
WORKDIR /home/rstudio/my-project
RUN R -e "renv::restore()"

*# Run targets
*RUN R -e "targets::tar_make()"
*# Render report
*RUN R -e "rmarkdown::render(input = 'documents/report.Rmd')"

# Change ownership
RUN chown -R rstudio:rstudio /home/rstudio/
```
]
]

---
# After the Development

.code-size-12[
```bash
#----    Dockerfile    ----
FROM rocker/rstudio:4.1.2

# Copy project files
COPY . /home/rstudio/my-project

# Install packages
WORKDIR /home/rstudio/my-project
RUN R -e "renv::restore()"

*# Run targets
*RUN R -e "targets::tar_make()"
*# Render report
*RUN R -e "rmarkdown::render(input = 'documents/report.Rmd')"

# Change ownership
RUN chown -R rstudio:rstudio /home/rstudio/
```
]
]
---
# Rocker as IDE

.pull-left-60[
.move-down-80[
#### Run Container
]

.code-size-12[
```bash
docker run --rm -p 8787:8787 -e DISABLE_AUTH=true \
    -v  ~/Desktop/My-project:/home/rstudio/my-project \
    rocker/verse:4.1.2
```
]
]
.pull-right-40[

]

---
# Rocker as IDE

.pull-left-60[
.move-down-80[
#### Run Container: renv Cache
]

.code-size-12[
```bash
docker run --rm -p 8787:8787 -e DISABLE_AUTH=true \
    -v  ~/Desktop/My-project:/home/rstudio/my-project \
    rocker/verse:4.1.2
```
]
]
.pull-right-40[
.move-down-80[
.code-size-12[
{{content}}
]
]
]

--
#### Host System

```
~/Docker/
    |-- renv-cache/
```

---
# Rocker as IDE

.pull-left-60[
.move-down-80[
#### Run Container: renv Cache
]

.code-size-12[
```bash
docker run --rm -p 8787:8787 -e DISABLE_AUTH=true \
    -v  ~/Desktop/my-project:/home/rstudio/my-project \
*   -v  ~/Docker/renv-cache:/home/rstudio/.cache/R/renv \
*   -e  RENV_PATHS_CACHE=home/rstudio/.cache/R/renv \
    rocker/verse:4.1.2
```
]
]
.pull-right-40[
.move-down-80[
.code-size-12[
#### Host System

```
~/Docker/
    |-- renv-cache/
```
]
]
]

---
# Rocker as IDE

.pull-left-60[
.move-down-80[
#### Run Container: GitHub Authentication
]

.code-size-12[
```bash
docker run --rm -p 8787:8787 -e DISABLE_AUTH=true \
    -v  ~/Desktop/my-project:/home/rstudio/my-project \
    -v  ~/Docker/renv-cache:/home/rstudio/.cache/R/renv \
    -e  RENV_PATHS_CACHE=home/rstudio/.cache/R/renv \
    rocker/verse:4.1.2
```
]
]
.pull-right-40[
.move-down-80[
.code-size-12[
#### Host System

```
~/Docker/
    |-- renv-cache/
```
]
]
]
---
# Rocker as IDE

.pull-left-60[
.move-down-80[
#### Run Container: GitHub Authentication
]

```
~/Docker/
    |-- renv-cache/
    |-- docker-gitconfig.txt
    |-- ssh-key
```
]
]
]
---
# Rocker as IDE

.pull-left-60[
.move-down-80[
#### Run Container: GitHub Authentication
]

```
~/Docker/
    |-- renv-cache/
*   |-- docker-gitconfig.txt
    |-- ssh-key
```

```
#----    gitconfig    ----#
[user]
        name = <username>
        email = <user-email>
[merge]
        conflictstyle = diff3
```

]
]
]

---
# Rocker as IDE

.pull-left-60[
.move-down-80[
#### Run Container: GitHub Authentication
]

.code-size-12[
```bash
docker run --rm -p 8787:8787 -e DISABLE_AUTH=true \
    -v  ~/Desktop/my-project:/home/rstudio/my-project \
    -v  ~/Docker/renv-cache:/home/rstudio/.cache/R/renv \
    -e  RENV_PATHS_CACHE=home/rstudio/.cache/R/renv \
*   -v  ~/Docker/ssh-key:/home/rstudio/.ssh\
*   -v  ~/Docker/docker-gitconfig.txt:/etc/gitconfig\
    rocker/verse:4.1.2
```
]
]
.pull-right-40[
.move-down-80[
.code-size-12[
#### Host System

```
~/Docker/
    |-- renv-cache/
    |-- docker-gitconfig.txt
    |-- ssh-key
```

```
#----    gitconfig    ----#
[user]
        name = <username>
        email = <user-email>
[merge]
        conflictstyle = diff3
```

]
]
]
---
class: inverse, center, middle

# Happily (and Reproducible) Ever After

## The End 🎉🎉