Essentials of Next Generation

E S S E N T I A L S O F N E X T G E N E R A T I O N S E Q U E N C I N G W O R K S H O P 2 0 1 5 U N I V E R S I T Y O F K E N T U C K Y A G T C

Class 1 Unix/Linux cheat sheet Navigation Commands 1. pwd print working directory (dir) - shows what dir you're in 2. ls list the contents of a dir 3. ls -l list the contents of a dir and show extra info about the files 4. ls -a list all files, including hidden files 5. cd change directory 6. cd .. go to the parent directory 7. cd ~ go to your home directory 8. exit log out of the current session 9. ↑,↓ scroll through command history 10. [tab key] autocomplete current command/filename 11. ctrl-a jump to the start of current command line 12. ctrl-e jump to the end of current command line

Help Commands 13. man read manual for a command 14. man –k search for manual page via a keyword 15. whereis x show locations for application x 16. which x show which application x will be run by default

Examining files 17. file determine the type of a file 18. cat concatenate a file 19. less view text files 20. head view first 10 lines of a file 21. head -n x view first x lines of a file 22. tail view last 10 lines of a file 23. tail -n x view last x lines of a file 24. grep locate a pattern in a file (or files)

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Manipulating files and directories 25. cp copy a file 26. cp -i copy a file and ask before overwriting

Essentials of Next Generation Sequencing 2015 Page 2 of 3 Manipulating files and directories (cont.) 27. cp -r copy a directory with its contents 28. mv x y move or rename a file x to y 29. mv -i move or rename a file and ask before overwriting 30. rm remove a file 31. rm -r remove a directory with its contents 32. rm -i ask before removing a file. Good to use with the -r option 33. mkdir make a directory 34. rmdir remove an empty directory 35. chmod change permissions of a file 36. sort sort files (merges too) (useful: --ignore-case and --key=x)

Internet 37. wget download a file 38. ssh connect via secure shell to a machine 39. scp upload/download files, examples: upload: scp local_source user@host:~/destination download: scp user@host:~/remote_source local_destination

Multi-tasking 40. ctrl+z stops whatever program you are using 41. bg lists stopped jobs; resumes the last stopped job and runs it in the background 42. jobs lists stopped or backgrounded jobs 43. fg brings most recent backgrounded job to the foreground 44. fg x brings job x to the foreground 45. ctrl+c terminates whatever program you are using (permanently)

Compression 46. tar -cvf create a tar archive 47. tar -xvf extract a tar archive 48. tar -czvf create a tar.gz (gunzip'ed) archive 49. tar -xzvf extract/unzip a tar.gz archive 50. zip zip a file 51. unzip un-zip a file 52. gzip gzip a file 53. gunzip un-gzip a file

Pipe tools 54. wc word-count (and lines, and bytes) 55. sort sort (by default on first column) 56. uniq merge repeated lines 57. tr translate characters 58. tee save intermediate results

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