sunnylt1/bioconductor-lyumengxian

bioconductor-lyumengxian created by GitHub Classroom

build bioconductor docker image

This assignment walks you through modifying an bioconductor docker images by installing asciinema and saving the new docker image to dockerhub. asciinema is a free and open source solution for recording terminal sessions and sharing them on the web. Docker is tool that packages software into self-contained computing environments, called containers. Docker Hub is a hosted repository service provided by Docker for finding and sharing container images with others.

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Learning Objectives:

• build a docker image
• create a screen-cast
• run the bioconductor/bioconductor_docker container via docker
• save changes to a new docker image
• push the new docker image to dockerhub

Assignment

1. Complete the assignment described below.
2. Upload a link to your dockerhub account.
3. Upload a link with screen-cast.

Prerequisites

• create an asciinema account using email at asccinema.org
• create a dockerhub account

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Assignment Points

Rubric	Points
Dockerhub	-/5
Screencast	-/5
On Time	-/5
Total Points: -/15

Getting Started

1. open docker teminal

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2. clone repo and navigate to directory

cd ~/bioconductor

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3. create a new container that installs asciinema using a dockerfile

docker build -t bioconductor_asciinema .

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4. boot into the new docker container

docker run -it bioconductor_asciinema:latest bash

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5. start a screen-cast from within the container

asciinema rec

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6. link your container to your asciinema.org account by opening the URL in a web browser

asciinema auth

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7. add screen-cast headers and check your docker container

# GMS6804
# name: [your-name-here]
# date: [current-date]
# semester: [current-semester]
# assignment: quiz07- bioconductor-asciinema  

# check if R is installed?
R
# check if bioconductor package installed:
library(Biostrings)
sequences <- c("AAATCGA", "ATACAACAT", "TTGCCA")
sequences
dna <- DNAStringSet(sequences)
dna
reverse(dna)
reverseComplement(dna)
quit()

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8. exit out of container

CTRL-D

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9. login to dockerhub

docker login
login: [YOUR DOCKERHUB ID]
pwd: [YOUR PASSWORD]

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10. tag container

docker tag bioconductor_asciinema [YOUR DOCKERHUB ID]/bioconductor_asciinema:[month_year]
docker push [YOUR DOCKERHUB ID]/bioconductor_asciinema:[month_year]