verse-gviz

rocker-verse container with Bioconductor Gviz

This (bloated) container is built on top of rocker/verse container so that genomic coordinate plots can be drawn with Gviz in Rstudio environment with reproducible manner. I needed such a container for teaching Data Analysis and Visualization course and Rmarkdown based publishing.

rocker/verse container includes:

version stable base R (smaller container size compared to r-base) and I used R version 3.4.1
Rstudio server
tidyverse & devtools
tex & publishing-related packages

How to use

Run the following command in terminal

docker run -d -p 8787:8787 alperyilmaz/verse-gviz

In the first run verse-gviz container will be downloaded and it might take time based on your internet connection. Following runs will be instant.

After running this command, go to your browser and visit http://localhost:8787 and you'll be greeted with Rstudio server login page. Both username and passwords are same which is rstudio. If needed be, rstudio server can be initiated with desired username and passwords with following command:

docker run -d -p 8787:8787 -e USER="studentno" -e PASSWORD="studentpass" alperyilmaz/verse-gviz

Play with Docker usage

UPDATE: In order to use Play with Docker, you need to login with a DockerID. Please sign up for one at Docker.com

If you're low on disk space, using Windows or having slow internet connection, then you can try or use this container online. The authors of Play With Docker site, Marcos Lilljedahl and Jonathan Leibiusky, made it possible to run containers online with breeze (if interested in technical details please watch their demo at DockerCon 2017).

In order to use this container with Play with Docker:

Please visit Play With Docker site
(1) Click on Add New Instance (occasionally this might freeze, if that happens please re-visit the site)
(2) On the terminal window, type docker run -d -p 8787:8787 alperyilmaz/verse-gviz and hit enter
(3,4) After the process finished successfully, you'll see a link 8787 on top of the page
When you click the link, you'll be at Rstudio server login page (username and passwords are rstudio)
(5) IMPORTANT While using play with docker the instances have certain time limit (4 hours at the time of writing this note). When an instance is killed all data will be lost. So please copy over unsaved data to your local folder or git push frequently to prevent loss of data.

Happy reproducible researching ;)