docker.Rmd

---
title: "Run in a Docker container"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Run in a Docker container}
  %\VignetteEngine{knitr::knitr}
  %\usepackage[UTF-8]{inputenc}
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

A dockerised version of <span style="color:#5793dd;vertical-align:top;font-size:90%;font-weight:normal;">sen</span><span style="color:#6a7077;vertical-align:baseline;font-size:115%;font-weight:bolder;">2</span><span style="color:#2f66d5;vertical-align:baseline;font-size:90%;font-weight:bold;">r</span> is available [here](https://hub.docker.com/r/ranghetti/sen2r): it contains a working RStudio environment with the package <span style="color:#5793dd;vertical-align:top;font-size:90%;font-weight:normal;">sen</span><span style="color:#6a7077;vertical-align:baseline;font-size:115%;font-weight:bolder;">2</span><span style="color:#2f66d5;vertical-align:baseline;font-size:90%;font-weight:bold;">r</span> and all its dependencies (both R packages and runtime dependencies). It can be used in order to avoid troublings about compiling all the required R packages, or in case of problems with runtime dependencies (typically GDAL over Windows).

To use it:

1. [install Docker CE](https://docs.docker.com/install) version 1.13 or higher;

2. read the docker documentation in [Part 1](https://docs.docker.com/get-started);

3. obtain the image of <span style="color:#5793dd;vertical-align:top;font-size:90%;font-weight:normal;">sen</span><span style="color:#6a7077;vertical-align:baseline;font-size:115%;font-weight:bolder;">2</span><span style="color:#2f66d5;vertical-align:baseline;font-size:90%;font-weight:bold;">r</span>:
    ```{bash, eval = FALSE}
    docker pull ranghetti/sen2r:latest
    ```
    where `latest` corresponds to the software version in branch [main](https://github.com/ranghetti/sen2r/tree/main) (see [here](https://hub.docker.com/repository/registry-1.docker.io/ranghetti/sen2r/tags) all the available docker tags);
    
4. run the docker:
    ```{bash, eval = FALSE}
    docker run --rm -e PASSWORD=sen2r -e USERID=$(id -u) -v $(pwd):/home/rstudio/host -p 8777:8787 ranghetti/sen2r
    ```
    where:
    
    - `-e PASSWORD=sen2r` is the password to be used to login;
    - `-v $(pwd):/home/rstudio/host` means that the current directory will be mounted in the docker, and its content will be available in the subdirectory `host` of the docker folder tree (to mount a different directory, replace `$(pwd)` with the desired directory);
    - `-p 8777:8787` means that the dockerised RStudio will be accessible from port 8777 (change it to use a different port).
    
5. access to the RStudio environment from `http://localhost:8777`, logging in with user `rstudio` and the password set as above;

6. for online use, add the user's SciHub credentials using the GUI or with the function:
    ```{r, eval = FALSE}
    library(sen2r)
    write_scihub_login("<scihub_username>", "<scihub_password>")
    ```