Getting Back Into Headless Cloud Computing

Use Case

This tutorial answers the question, “How do I log back into a remote server and analyze data without a graphical user interface, again?”

This is adapted from some notes I used when I was several months into a bioinformatics class and wanted to pick back up where I’d left off in the headless cloud environment.

Since not all setups will be identical, and having several tools setup already is a prerequisite for this workflow, see the bottom of this post for my dependencies.

Login

  • Open VPN app on your PC, e.g. Global Protect
  • Enter your institutional account’s username and password
  • Open Git Bash and initialize SSH connection
  • Provide server-specific username and password, given to you by your instructor or IT admin for cloud computing
  • e.g. ssh Last_Name_Example@server_name.insitution.edu -p port_number; enter provided password

Shorten bash prompt

  • Often, the bash prompt becomes unwieldy in length
  • Try shortening it to just user and path: PS1='\u:\W\$ '
  • Or, just path: PS1='\W\$ '

Configure git in container

  • Find the right folder: ~
  • Clone git clone https://github.com/user/repo
  • Set user git config --global user.name “Full Name”
  • Set email git config --global user.email “preferred@email.com”
  • Create new branch git branch example-branch
  • Switch to new branch git checkout example-branch
  • Add something, e.g. README git add README.md
  • Commit git commit -m “Initialize example branch”
  • Uncommit git reset --soft HEAD~1
  • Push git push
  • Enter GitHub username and password
  • Check git config --list

Restore git session from different machine

  • Pull down changes made on the same branch git pull
  • Pull down changes made on branch master on the remote origin and integrate them into your local HEAD branch: git pull origin master
  • List branches git branch -a
  • Switch to a branch git checkout example-branch

Manage persistent work sessions

Tmux is essential in bioinformatics, where genome sequence files can be massive and take hours or days to process. Tmux creates a resilient work session that persists and will process your data continuously, even if the SSH connection is closed. It has a great [cheat sheet][cs]. It is also the topic of a great independent [blog post][tmuxblog].

  • List any open sessions tmux ls
  • Attach to existing session tmux a <session if more than one>
  • Create new session tmux new -s session-name
  • Kill a section tmux kill-ses -t session-name
  • Split pane vertically ctrl+b, %
  • Split pane horizontally ctrl+b, ”
  • Switch panes ctrl+b, o
  • Close current pane ctrl+b, x
  • Detach from session ctrl+b, d

Build a bash script in nano

  • Create empty script touch script_name.sh
  • Open script nano script_name.sh

  • Proceed with your analysis!

    Dependency information for this tutorial

  • Institutional login: [University of San Francisco][usf]
  • The University of San Francisco hosts several servers available to graduate and undergraduate students. I am a biotechnology Master’s student, class of 2022.
  • VPN: [Global Protect][global-protect] for Windows 10
  • Many institutions require virtual private networks to login to their servers, allowing your workstation to imitate a local machine for cluster access.
  • git version control: [GitHub][github]
  • bash shell: [Git Bash][git-bash]
  • Session management: [Tmux][tmux]
  • Container admin: [Docker][docker]
  • SSH credentials: contact your IT admin
  • Instruction: Dr. Naupaka Zimmerman. Check out his extensive [GitHub page][drz] [usf]: https://www.usfca.edu/arts-sciences/graduate-programs/biotechnology [global-protect]: https://www.paloaltonetworks.com/products/globalprotect [github]:[https://github.com/] [git-bash]:[https://gitforwindows.org/] [tmux]:[https://github.com/tmux/tmux/wiki] [tmuxblog]:[https://github.com/2020F-usfca-btec-640/2020F-usfca-btec-640.github.io/blob/main/_posts/2020-11-07-What-is-Tmux.md] [cs]:[https://tmuxcheatsheet.com/] [docker]:[https://www.docker.com/] [drz]:[https://github.com/naupaka]