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https://github.com/reconhub/docker

Various docker images for RECON
https://github.com/reconhub/docker

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Various docker images for RECON

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RECON docker images

===================



What is this?

-------------



[Docker](https://www.docker.com/what-docker) provides a robust, lightweight way

to ship applications within a small, self-sufficient operating system, which

includes all the dependencies and tools required for the app the run

smoothly. This structure is called a *container*, and different versions of a

container are referred to as *images*.



The major advantage of using this system to deploy a set of applications is that

applications are guaranteed to work the same for every user, regardless of their

operating system or system settings. For RECON packages, this means that you do

not need to worry about using the right R version, or installing packages and

their dependencies, because the RECON docker image will contain all this

already.



Several RECON docker images will be developed. The default one will always be

`reconhub/recon`.



How can I use it?

-----------------



### Installing docker



First of all, you need docker installed on your computer. Follow [this

link](https://www.docker.com/community-edition#/download) for guidelines to

install Docker Community Edition.



Then you need to choose the RECON docker image you want to use (see next

sections on available images), and choose how you want to use the image. There

are **two recommended ways** to use RECON docker images: starting a **Rstudio

server**, or starting a **bash session**.



### Rstudio server 



This approach is aimed at regular users, is the use the image to start a Rstudio

server, which enable the user to start a Rstudio session within a web browser,

with all currently functional RECON packages and their dependencies

pre-installed. In short: you will be able to use the RECON packages without even

installing R or Rstudio. See an example of such session using the package

[*epicontacts*](http://www.repidemicsconsortium.org/epicontacts/):



![recon rstudio session](img/recon_rstudio.jpg)



Importantly, you can also start the RECON GUI from this session. For instance,

to start the incidence GUI, you only need typing `incidence.ui::incidence_ui()`:



![incidence GUI](img/incidence_ui.jpg)



This image is started by typing:

```

docker run -d -p 8787:8787 reconhub/recon

```



where `reconhub/recon` can be replaced by your preferred RECON docker image. A

Rstudio session can then be started by opening a web browser and going to the

URL `127.0.0.1:8787` (or `localhost:8787`). The login and password are

'rstudio'.



### `bash` session



This approach is recommended for developers. It will open a `bash` shell logged

as `guest` within the `/home/guest`. A folder `/home/guest/dev` will contain git

clones of the various installed packages. A R session can be started (without

support for graphics) simply by typing `R`.



To start the docker image with a `bash` shell, type:

```

docker run --rm -it --user guest reconhub/recon /bin/bash

```



where `[image]` is the docker image you want to use. 



Available docker images

-----------------------



A list of available images can be found from the [RECON docker repository](https://hub.docker.com/u/reconhub/dashboard/).



### Default image: `reconhub/recon`



#### Description



This image contains all functional RECON packages. CRAN versions are installed

when available, otherwise github versions are used. It also contains package

sources for testing. It is based on

[rocker/verse](https://hub.docker.com/r/rocker/tidyverse/)



#### Content summary



- CRAN packages: *outbreaks*, *incidence*, *epicontacts*



- github packages: *epicontacts*, *distcrete*, *outbreaker2*, *vimes*,

*shinyHelpers*, *recon.ui*, *incidence.ui*, *epicontacts.ui*



- users: 'guest' (for bash session) and 'rstudio' (for Rstudio session) 



- package sources: git-cloned in `/home/guest/dev/`



### Devel image: `reconhub/devel`



#### Description



This image designed for testing is based on daily snapshots of R-devel from

[rocker/drd](https://hub.docker.com/r/rocker/drd). It also

contains all the sources of the packages cloned from github.



**Note**: unless you need to test a package on R-devel, prefer using the more

  reliable default image (reconhub/recon).



#### Content summary



- github packages: *outbreaks*, *incidence*, *epicontacts*, *distcrete*,

*outbreaker2*, *vimes*, *shinyHelpers*, *recon.ui*, *incidence.ui*,

*epicontacts.ui*



- users: 'guest' (for bash session)



- package sources: git-cloned in `/home/guest/dev/`



Contributions

-------------



Contributors (by alphabetic order):

- [Thibaut Jombart](https://github.com/thibautjombart)



See details of contributions on:




https://github.com/reconhub/docker/graphs/contributors



Contributions are welcome via **pull requests**.



Please note that this project is released with a [Contributor Code of

Conduct](CONDUCT.md). By participating in this project you agree to abide by its

terms.



**Maintainer:** Thibaut Jombart ([email protected])