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Docker Image for HaplotypR

Colby T. Ford, Ph.D.

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

DockerHub

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

Pull Image to Local Machine

docker pull cford38/haplotypr:latest

To Run Locally

docker run --name haploytypr --rm -p 8787:8787 cford38/haplotypr
#docker exec -it haplotypr /bin/bash

Copy File to Container

docker cp myfile.txt haplotypr:./myfile.txt

Copy Files from Container

docker cp haplotypr:./root/haplotypr/ ./

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 haplotypr .

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

  1. Once the image has been created successfully, run the container using the following command.
docker run --name haploytypr --rm -p 8787:8787 haplotypr

Then, navigate to localhost:8787 from your web browser.

Push to DockerHub

docker image tag haplotypr <USERNAME>/haplotypr:latest
docker push <USERNAME>/haplotypr:latest

About HaplotypR

HaplotypR, developed by Anita Lerch, Ph.D. at the University of Notre Dame, is a program for analysis of Amplicon-Seq genotyping experiments. Check out her website for more details: [https://lerch-a.github.io/HaplotypR/)