2015 11-10-bio-in-docker-oswitch
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This document describes oSwitch, a tool that allows easy access to other operating systems via one-line commands. It works by wrapping Docker containers, allowing commands to be run in different OS environments without disrupting the user's current environment. The document provides an example usage where a user is able to run an "abyss-pe" command in a Biolinux container after it is not found in their native OS. It notes how oSwitch aims to preserve the user's current working directory, login shell, home directory and file permissions during usage.
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2015 11-10-bio-in-docker-oswitch
- 1. oSwitch - easily access other operating systems y.wurm@qmul.ac.uk http://wurmlab.github.io 2015-11-10-DockerInBio
- 2. © Alex Wild & others
- 4. © National Geographic Atta leaf-cutter ants
- 5. © National Geographic Atta leaf-cutter ants
- 6. © National Geographic Atta leaf-cutter ants
- 8. Oecophylla Weaver ants © ameisenforum.de
- 10. © ameisenforum.de Oecophylla Weaver ants
- 12. Tofilski et al 2008 Forelius pusillus
- 13. Tofilski et al 2008 Forelius pusillus hides the nest entrance at night
- 14. Tofilski et al 2008 Forelius pusillus hides the nest entrance at night
- 15. Tofilski et al 2008 Forelius pusillus hides the nest entrance at night
- 16. Tofilski et al 2008 Forelius pusillus hides the nest entrance at night
- 17. Avant Workers staying outside die « preventive self-sacrifice » Tofilski et al 2008 Forelius pusillus hides the nest entrance at night
- 18. Dorylus driver ants: ants with no home © BBC
- 20. Animal biomass (Brazilian rainforest) from Fittkau & Klinge 1973 Other insects Amphibians Reptiles Birds Mammals Earthworms Spiders Soil fauna excluding earthworms, ants & termites Ants & termites
- 21. Well-studied: • behavior • morphology • evolutionary context • ecology Genetic basis? https://wurmlab.github.io
- 22. This changes everything. Any lab can sequence anything!
- 23. Major challenges for genomics data handling data analysis visualisation Opportunities
- 25. http://wurmlab.github.io • Understanding/visualising/massaging data is hard. • Biology/life is complex. • Field is young. • Biologists lack computational training. • Analysis tools (generally) suck: • badly written • badly tested • hard to install • output quality… often questionable. • Data sizes keep growing! • Data formats keep changing :( Genome bioinformatics is hardGenome bioinformatics is harder than (many) other data sciences New dataset. Which of 10 tools that should do X can actually do X. Hours to months!
- 32. http://wurmlab.github.io • Understanding/visualising/massaging data is hard. • Biology/life is complex. • Field is young. • Biologists lack computational training. • Analysis tools (generally) suck: • badly written • badly tested • hard to install • output quality… often questionable. • Data sizes keep growing! • Data formats keep changing :( Genome bioinformatics is hardGenome bioinformatics is harder than (many) other data sciences
- 33. oSwitch
- 34. oSwitch - one-line operating system switching oSwitch
- 35. EOS Cloud Bruno Vieira @bmpvieira Anurag Priyam @yeban https://github.com/wurmlab/oswitch Tim Booth @tbooth
- 36. https://wurmlab.github.io oSwitch is just a small wrapper around Docker
- 37. http://wurmlab.github.io oSwitchOne-line access to other operating systems. mymac:~/2015-‐06-‐01-‐project> abyss-‐pe k=25 reads.fq.gz zsh: command not found: abyss-‐pe mymac:~/2015-‐06-‐01-‐project> oswitch -‐l yeban/biolinux:8 ubuntu:14.04 ontouchstart/texlive-‐full ipython/ipython mymac:~/2015-‐06-‐01-‐project> oswitch yeban/biolinux ###### Now running: biolinux in container biolinux-‐7187 biolinux-‐7187:~/2015-‐06-‐01-‐project> abyss-‐pe k=25 reads.fq.gz [... just works on your files where they are...] biolinux-‐7187:~/2015-‐06-‐01-‐project> exit ###### Back to your host OS ###### mymac:~/2015-‐06-‐01-‐project> [... output is where you expect it to be ...] Or use in one-line e.g.: oswitch biolinux bwa aln -t 48 genome.fna reads.fq
- 38. https://wurmlab.github.io Things feel (largely) unchanged: •Current working directory •Login shell (bash/zsh/fish) •User name, uid and gid •Home directory (.dotfiles are respected). •Paths (when possible) - host-mounted volumes (drives, NAS, USB) available in the container at the same path. •read/write permissions. oSwitch One-line access to other operating systems. https://github.com/wurmlab/oswitch
- 40. https://wurmlab.github.io Helps: • Save installation time (researchers, sysadmins) • Determining which of 10 tools that should do X can actually do X. • Reproducibility via project-specific Dockerfiles • http://software.ac.uk Benefits greatly from this community (bioboxes, ngseasy, nucleotid.es, etc.) oSwitch switching
- 41. https://wurmlab.github.io oSwitch is just a small wrapper around Docker
- 46. https://wurmlab.github.io Open issues on github.
- 47. https://github.com/wurmlab/oswitch EOS Cloud Bruno Vieira @bmpvieira Anurag Priyam @yeban Tim Booth @tbooth Thanks! Richard Nichols (QMUL), David Wallom (Oxford), Peter Kille (Cardiff) Tom Meagher (St Andrews), Dawn Field (CEH Wallingford)