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Creating Docker container

Docker is a service for finding and sharing container images with your team

Docker installation

For instaling Docker Desktop for MacOs click the link Docker and follow instructions

Docker usage

  1. Sign up for Docker
  2. Create a new repository on the Docker webpage
  3. Open the terminal and sign in to Docker Hub on your computer $ docker login
  4. Build and push a container image to Docker Hub from your computer

    • Create a dockerfile with your application

        cat > Dockerfile <<EOF 
  from busybox 
  CMD echo "Hello world! This is my first docker image." 
  EOF

    • Build a docker image

      docker build -t <your_username>/my-first-repo .
docker build -t dianacornejo/new-repo .

    • Run the docker image with bash

      docker run -t -i --rm dianacornejo/new-repo bash

    • Create shared folders between host and container (example with standard image)

      docker run -it -v ~/test:/home/jovyan/work/ statisticalgenetics/lmm:1.3 bash

    • Remove images, containers and all the things that take space docker system prune --all --force --volumes

Useful docker commands to keep in mind

  • docker log in

  • docker build -t NAME[:TAG] -f [PATH/dockerfile name] .. Example: docker build -t statisticalgenetics/nps-1.1:1.1 -f ./nps.dockerfile .

  • docker push OPTIONS NAME[:TAG]. Example: docker push statisticalgenetics/nps1.1 or docker push statisticalgenetics/nps-1.1:1.1 to push an specific tagged version

You can build the docker containers if you have the statgen-setup script created by Gao simply writing:

  • statgen-setup build --tutorial nps --tag <version number>. Using this script the image is build and pushed to dockerhub so no further steps are necessary.

  • statgen-setup launch --tutorial [NAME] --my-name [USER_NAME]. This command is used to lauch a container from a docker image already created and uploaded to the repository.

  • statgen-setup login --tutorial [tutorial name] --my-name [diana]. Example: statgen-setup login --tutorial nps --my-name diana Use this command to run a specific tutorial. Don't forget to use a unique name.

  • statgen-setup clean. To shutdown all containers and clean up the dangling ones. Run as a root. You should do this before building a new container and running it, so the changes in the dockerfile can take place.

  • docker pull NAME[:TAG]. Example: docker pull statisticalgenetics/nps-1.1:1.1 This command pulls an image from a repository

  • docker run OPTIONS NAME[:TAG]. Example: docker run -it statisticalgenetics/nps-1.1:1.1 -i: interactive (Keep STDIN open even if not attached) and -t: Allocate a pseudo-TTY.

  • docker images ls To list all the created images

  • docker image rmi [image-number] To delete the image you are specifying, option -f to force removal

  • docker ps -a For a list of all running containers

  • docker stop [container id] To stop a specific container

  • docker container stop $(docker container ls -aq) To stop all running containers

Creating a container for annovar in statgen-courses

Being in the ~/statgen-course/docker folder run the following command:

  1. Create the DockerFile as the example below: vim annovar.dockerfile

FROM ubuntu:latest This command specifies de base image to derive from

MAINTAINER Diana Cornejo <[email protected]> This command indicates who created the image

WORKDIR /root This command is to specify the working directory

#Install dependency tools and deploy data-set package that Carl made RUN echo "deb [trusted=yes] http://statgen.us/deb ./" | tee -a /etc/apt/sources.list.d/statgen.list && \ apt-get update && \ apt-get install -y annotation-tutorial && \ apt-get clean

The above commands indicate the .deb package to install in this case annovar from what Carl had prepared earlier http://statgen.us/deb/

## Update the exercise text ARG DUMMY=unknown RUN DUMMY=${DUMMY} curl -fsSL https://raw.githubusercontent.com/statgenetics/statgen-courses/master/handout/FunctionalAnnotation.2019.docx

  1. Build the docker image: You have to specify the path where your dockerfile is located to be able to create the image

docker build -t statisticalgenetics/annovar -f ./annovar.dockerfile . -t indicates tag, -f the file from which you wish to creater the docker image and the . to create the image.

docker build -t statisticalgenetics/annovar:0.1.0 -f ./annovar.dockerfile . If you want to tag the docker image add : and then the version number

docker build --build-arg DUMMY='date +%s' -t statisticalgenetics/nps1.1 -f docker/nps.dockerfile docker You can also set build-time varirables and specify them when creating the image.

  1. Push built image into dockerhub: That way anyone can pull the image and use it

docker push statisticalgenetics/annovar Without tags docker push statisticalgenetics/nps1.1:1.1 With tags

statgen-setup login --tutorial annovar --my-name diana This step will allow you to run the different tutorials on the cloud

  1. Test the command line

Start the tutorial as is written in the exercise

Creating a docker container for the Regression exercise.

This is based on Carl's deb packages

  1. Create the docker file
FROM gaow/base-notebook:latest

MAINTAINER Diana Cornejo <[email protected]>

USER root

#Install dependency tools and install data-set

RUN echo "deb [trusted=yes] http://statgen.us/deb ./" | tee -a /etc/apt/sources.list.d/statgen.list && \
apt-get update && \
    apt-get install -y regression-tutorial && \
    apt-get clean && mv /home/shared/* /home/jovyan && chown jovyan.users -R /home/jovyan/*

#Download notebook script and clean out output

USER jovyan
ARG DUMMY=unknown
RUN DUMMY=${DUMMY} curl -fsSL https://raw.githubusercontent.com/statgenetics/statgen-courses/master/handout/regression.docx -o regression.docx
RUN curl -fsSL https://raw.githubusercontent.com/statgenetics/statgen-courses/master/handout/regression.pdf -o regression.pdf
  1. Build the docker image

docker build -t statisticalgenetics/regression -f ./regression.dockerfile .

  1. Push the image into dockerhub

docker push statisticalgenetics/regression

statgen-setup login --tutorial regression --my-name diana

  1. Test the command line

Based on the exercise test that it runs

Create a docker container for the population drift and selection exercises

This is based on Carl's deb packages

  1. Create de dockerfile
ROM gaow/base-notebook:latest
  
MAINTAINER Diana Cornejo <[email protected]>

USER root

#Install dependency tools and install data-set using Carl's deb packages

RUN echo "deb [trusted=yes] http://statgen.us/deb ./" | tee -a /etc/apt/sources.list.d/statgen.list && \
apt-get update && \
    apt-get install -y popgen-tutorial && \
    apt-get clean && mv /home/shared/* /home/jovyan && chown jovyan.users -R /home/jovyan/*

#Download scripts and tutorial files

USER jovyan
ARG DUMMY=unknown
RUN DUMMY=${DUMMY} curl -fsSL https://raw.githubusercontent.com/statgenetics/statgen-courses/master/handout/PopGen.docx -o PopGen.docx
RUN DUMMY=${DUMMY} curl -fsSL https://raw.githubusercontent.com/statgenetics/statgen-courses/master/handout/PopGen.pp.docx -o PopGen.pp.docx
RUN curl -fsSL https://raw.githubusercontent.com/statgenetics/statgen-courses/master/handout/PopGen.pp.pdf -o PopGen.pp.pdf
RUN curl -fsSL https://raw.githubusercontent.com/statgenetics/statgen-courses/master/handout/PopGen.sim.docx -o PopGen.sim.docx
RUN curl -fsSL https://raw.githubusercontent.com/statgenetics/statgen-courses/master/handout/PopGen.sim.noscript.docx -o PopGen.sim.noscript.docx
RUN curl -fsSL https://raw.githubusercontent.com/statgenetics/statgen-courses/master/handout/PopGen.sim.noscript.pdf -o PopGen.sim.noscript.pdf
RUN curl -fsSL https://raw.githubusercontent.com/statgenetics/statgen-courses/master/handout/PopGen.sim.pdf -o PopGen.sim.pdf
RUN curl -fsSL https://raw.githubusercontent.com/statgenetics/statgen-courses/master/code/popgen_drif.R -o popgen_drift.R
RUN curl -fsSL https://raw.githubusercontent.com/statgenetics/statgen-courses/master/code/popgen_selection.R -o popgen_selection.R
  1. Build the docker image

docker build -t statisticalgenetics/popgen -f ./popgen.dockerfile .

  1. Push the image into dockerhub

docker push statisticalgenetics/popgen

statgen-setup login --tutorial popgen --my-name diana

  1. Test the command line

Based on the exercise test that it runs