https://github.com/joey711/dada2docker
Docker build instructions for DADA2 and related functionality
https://github.com/joey711/dada2docker
Last synced: 4 months ago
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Docker build instructions for DADA2 and related functionality
- Host: GitHub
- URL: https://github.com/joey711/dada2docker
- Owner: joey711
- License: gpl-3.0
- Created: 2017-07-29T17:08:41.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2017-07-30T16:27:00.000Z (over 7 years ago)
- Last Synced: 2024-08-13T07:14:20.576Z (8 months ago)
- Language: R
- Size: 23.4 KB
- Stars: 3
- Watchers: 4
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Docker DADA2
This repo contains docker build instructions for images:
- [base](https://github.com/joey711/dada2docker/tree/master/base) -- release version of dada2 -- [joey711/dada2-base](https://hub.docker.com/r/joey711/dada2-base/)
- [base-devel](https://github.com/joey711/dada2docker/tree/master/base-devel) -- development [version of dada2](https://github.com/benjjneb/dada2) -- [joey711/dada2-base-devel](https://hub.docker.com/r/joey711/dada2-base-devel/)
- [rstudio-devel](https://github.com/joey711/dada2docker/tree/master/rstudio-devel) -- RStudio Server image with devel dada2 -- [joey711/dada2-rstudio-devel](https://hub.docker.com/r/joey711/dada2-rstudio-devel/)
- [shiny-devel](https://github.com/joey711/dada2docker/tree/master/shiny-devel) -- Shiny-dada2 app pre-installed on Shiny-Server image -- [joey711/dada2-shiny-devel](https://hub.docker.com/r/joey711/dada2-shiny-devel/)
## Quick Start
1. [Install Docker](https://docs.docker.com/engine/installation/) if you haven't already.
2. `docker run joey711/dada2-`
3. When done: do `CTL-C` at the terminal, or `docker container kill `. `docker container ls` will show you the container name.
## Shiny-rstudio
To host RStudio Server with dada2-devel pre-installed
```
docker run -d -p 8787:8787 -v ~:/home/rstudio/ joey711/dada2-rstudio-devel
```
- Where `~` can be replaced by a local (host) directory of your choice.
- You can also add `-v` args for making additional folders available in your Rstudio session.
- Point a browser window to `0.0.0.0:8787` while the container is running to start working in RStudio.
## Shiny-dada2
The run invocation has the following pattern (see the included runshinydada2.sh file for additional tips):
```
docker run --rm -p 3838:3838 \
-v ~/Downloads/:/home/rstudio/Downloads/ \
joey711/dada2-shiny-devel
```
- Where `~/Downloads/` should be replaced by a data directory on your machine that you want to "explore" with Shiny-dada2.
- Point a browser window to `0.0.0.0:3838` while the container is running.