https://github.com/hohonuuli/qiime1
Docker container for running qiime
https://github.com/hohonuuli/qiime1
docker qiime
Last synced: 2 months ago
JSON representation
Docker container for running qiime
- Host: GitHub
- URL: https://github.com/hohonuuli/qiime1
- Owner: hohonuuli
- Created: 2017-03-11T00:54:33.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2021-05-07T18:04:57.000Z (about 4 years ago)
- Last Synced: 2025-02-04T21:45:52.852Z (4 months ago)
- Topics: docker, qiime
- Size: 6.84 KB
- Stars: 3
- Watchers: 3
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
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README
# qiime1
[Docker](https://www.docker.com/) container with [Anaconda](https://www.continuum.io/), [qiime](http://qiime.org/), [R](https://www.r-project.org/), [Java](http://openjdk.java.net/), [RDP Classifier](https://github.com/rdpstaff/classifier), [ChimeraSlayer](http://microbiomeutil.sourceforge.net/), [Mothur](https://www.mothur.org/), [Muscle](http://www.mybiosoftware.com/muscle-3-8-31-multiple-sequence-alignment.html), [rtax](http://qiime.org/tutorials/rtax.html), and [Swarm](https://github.com/torognes/swarm).
It's a beast of a Docker container.
## Usage
To start an interactive session, first start a bash shell into the container.
```
docker pull mbari/qiime1
docker run --name qiime1 -v /Path/to/data:/mnt/data -i -t mbari/qiime1 /bash/bin
```
Once inside the container you just need to run:
```
source activate qiime1
# Your data will be in /mnt/data if you used the docker run command above
```