colbyford / seekdeep-docker

Repository for running SeekDeep in a Docker Container

Docker Image for SeekDeep

Colby T. Ford, Ph.D.

This repository contains the Dockerfile for generating an Ubuntu image with SeekDeep pre-installed.

DockerHub

This container image is available from DockerHub: hub.docker.com/r/cford38/seekdeep

Pull Image to Local Machine

docker pull cford38/seekdeep:latest

To Run Locally

docker run --name seekdeep -p 9881:9881 -d cford38/seekdeep
docker exec -it seekdeep /bin/bash

Copy File to Container

docker cp myfile.txt seekdeep:./myfile.txt

Copy Files from Container

docker cp seekdeep:./root/SeekDeep/ ./

---

Build Instructions

1. Clone this repository to your local machine

2. Open terminal and navigate to the directory of this repository.

3. Run the following command. This will generate the Docker image.

docker build -t seekdeep .

Note: You may have to increase the resource limits in Docker's settings as this container size (and the resources SeekDeep needs to run) will be quite large.

4. Once the image has been created successfully, run the container using the following command.

docker run --name seekdeep -it -p 9881:9881 -d seekdeep

5. Once the container is ready, remote into the bash terminal.

docker exec -it seekdeep /bin/bash

Note, from the terminal (and after you've completed your analysis), you can run the popClusteringViewer to browse through your results.

SeekDeep popClusteringViewer --verbose --configDir "$(pwd)/serverConfigs" --bindAddress 0.0.0.0 --port 9881 --name pcv

Then, navigate to localhost on your local browser. You should then be able to see the viewer tool.

---

To Publish on DockerHub

docker image tag seekdeep <USERNAME>/seekdeep
docker push <USERNAME>/seekdeep

---

About SeekDeep

SeekDeep, developed by the Bailey Lab at Brown University, is a suite of bioinformatics tools for analyzing targeted amplicon sequencing. Check out their website for more details: http://seekdeep.brown.edu/