12/17/2019 - (last updated: 2019-12-19)

Tutorials link

Quick reminders

  • add --rm to automatically delete container when done

  • pull images and use appropriate tag if necessary

  • We can run a container from:
    • within ("dive-in) or
    • without (“remote”)

Part 4: Learning objectives

Explore graphical options in specific docker images

  • Web-based

  • X11

Web-based

We’ll use 3 Docker images with Web interface:

  • NGINX: Web server
  • Dovex: python-based tabular data-explorer
  • RStudio server

Web-based - info

  • web-based means an http server
  • web files are stored in /usr/share/nginx/html

Local computer web address:

  • localhost
  • 127.0.0.1

Web-based - Ports

  • A container is like a black box…



  • … So we have to open “ports”
    of communication

Reserved / Standard ports

  • sftp: 21
  • ssh : 22
  • http: 80

We’ll use “port mapping” to connect Container ports to Local computer ports in docker run command:

  • Random assignment (-P)
  • Specific assignment (-p)

Web-based: NGINX

cd $HOME/dockershare

cat > mytestfile.html <<- EOF
<h1>My Test</h1>
<p>This is a simple HTML file.</p>
EOF

Results in:

Web-based: Dovex

Iris data set page.

Dovex home screen

Web-based: Dovex

Iris PCA analysis

Web-based: RStudio server

rstudio sign in

rstudio interface

New docker run commands

  • -d or --detach: run container in background (prompt back)
  • -P or --publish-all: publish all exposed ports to random ports
  • -p or --publish list: publish list of ports
  • --name: assign a name to the container
  • 2 methods to stop container with running process not in background:
    • Ctrl + C
    • docker stop ID - ID obtained with docker ps or docker container ls

:)










X11 is also called
“the X Windows system”

X11 - 3 images

We’ll use 3 Docker images with X11 interface:

  • IGV: java-based genome viewer
  • X11 utilities (some are fun)
  • EMBOSS Sequence analysis programs with interactive graphics

X11: IGV

X11: fun utilities

X11: EMBOSS

EMBOSS with interactive graphics: plotorf and tmap

X11 new commands

X11 display needs to be let through the local computer system

X11 - xhost

xhost can add (and delete) host names allowed to make connections to the X server. - From the local terminal:

xhost + localhost

localhost being added to access control list

Verify list:

xhost

access control enabled, only authorized clients can connect
INET6:localhost
INET:localhost

Note: remeber that 127.0.0.1 is also localhost

Getting Started

Reminder

  • Find Terminal in /Applications/Utilities
  • or use Spotlight (top right magnifying glass) and start typing Terminal

bash reminder:

$HOME is a variable representing your home directory, e.g. /Users/yourname

Colored backgrounds

“Where we are looking” within a Terminal:

Green: 
Commands from local computer terminal
Pink/Plum: 
Ligh plum background: commands from ALTERNATE local computer bash terminal
Blue: 
Commands and output when WITHIN Docker container
Yellow: 
Informational - DO NOT RUN! - commands or output examples.
White: 
generic output

Credits