Using Computers

1. Using Computers orSlowly going insane

2. UNIX Rapidly going insane

3. Your analyze Account • This is your own personal account • You are responsible for how it is used • DO NOT give out your username and password! • Peoples careers depend on use of the analyze

4. Screwing Up • Easy to do. • Frequently, the best way to learn. • Make a record of what happened. • Select appropriate lines • Save as a file, or print it out.

5. Help!!! • On analyze • analyze% genhelp • analyze% genmanual • GCG commands • analyze% man • UNIX • Web-based • Me (Elliot)

6. SeqLab Help Xwindows interface

7. SeqLab Help

8. SeqWeb Help gcg.genome.uab.edu

11. SeqStore Help http://gcg.genome.uab.edu:8050/seqstore_cgi/user_home.cgi

14. Elliot Help • E-mail to ElliotL@uab.edu • Phone: 4-1946 • See me in person (BBRB 277A) • Call First • Make an appointment

15. Analyze • Sun E450 UNIX server • UNIX: The Operating System • analyze runs Solaris 8

16. Logging On • Telnet to gcg.genome.uab.edu • Username: • Password: • System Announcements • Mail Messages

18. Logging Out • Finished. I want to go home. • analyze% logout

19. Login Messages SunOS 5.8 login: abel Password: Last login: Tue Apr 3 11:14:13 from GENWORK0 Sun Microsystems Inc. SunOS 5.8 Generic February 2000 ************** UAB Molecular and Genetic Bioinformatics Facility For help contact Elliot Lekfowitz (205) 934-1946 ELLIOTL@uab.edu or visit our web site: http://www.genome.uab.edu/ ************** MIC753 - Practical Applications of Sequence Analysis analyze%

20. Changing your password • analyze% passwd analyze% passwd Changing password for lefkowit. Old password: New password: Retype new password: analyze%

21. Start-Up Procedure • The files .login and .cshrc are automatically executed • They initialize various parameters • Terminal settings • GCG environment • .login • login script • .cshrc • C shell script

22. .login analyze% cat .login # @(#)local.login 1.5 98/10/03 SMI stty -istrip setenv TERM 'vt100' # # if possible, start the windows system. Give user a chance to bail out # if ( "`tty`" == "/dev/console" ) then if ( "$TERM" == "sun" || "$TERM" == "sun-color" || "$TERM" == "AT386" )n if ( ${?OPENWINHOME} == 0 ) then setenv OPENWINHOME /usr/openwin endif

23. .login echo "" echo -n "Starting OpenWindows in 5 seconds (type Control-C to i" sleep 5 echo "" $OPENWINHOME/bin/openwin clear # get rid of annoying cursor rectangle logout # logout after leaving windows system endif endif source /usr/local/uab_mic_environ.login

24. Changing your .login file • Can "personalize" your computer interactions • Specify the terminal you are using • setenv TERM vt100 • Execute commands • gcgff • gcgrdb

25. .cshrc analyze% cat .cshrc # @(#)cshrc 1.11 89/11/29 SMI umask 022 set path=(/bin /usr/bin /usr/ucb /etc /usr/local/bin /usr/dt/bin .) set path=(/usr/lib/lvm /etc/lvm /opt/SUNWspro/bin $path) if ( $?prompt ) then set history=32 endif alias h history alias edit /usr/dt/bin/dtpad alias acroread /opt/Acrobat4/bin/acroread alias lo logout limit coredumpsize 0

26. The Command Prompt analyze% • Type your commands following the prompt • Different UNIX shells use different prompts

27. Entering Commands • Type command at the analyze% prompt • Edit with the delete/backspace key • Hit Return • Sends command to the computer

28. Case (Upper and Lower) • Commands and names are case SENSITIVE • True for all UNIX computers • Type most commands in lower case • GCG commands must be typed in lower case • GCG qualifiers can be upper or lower case

29. Entering Multiple Commands on One Line • Separate each command with a semicolon ; analyze% ls ; pwd ; cd users; ls; pwd DXterm core.txt login.com mic733 src bin fastgbs login.com.bak nsmail users blast.sdbs gcg lookup.list out /disk01/users/lefkowit lgw old sullender uugen /disk01/users/lefkowit/users analyze%

30. Running in the Background • Commands or programs can be executed in the background • Allows you to return to the analyze% prompt and do something else • Enter an & at the end of the command and hit return • analyze% seqlab &

31. Long Commands • Take up more than one line • At the end of the first line type a backslash: \ • Hit return • Start typing on the second line

32. Long Commands analyze% map -infile=gendocdata:ggamma.seq –data \ enzyme.dat -once -six -cir

33. history • List your most recently used commands • Replay a command with !# • # is the command number as shown in the history list

34. history analyze% history 1 cat .login 2 cd 3 pwd 4 touch test.txt 5 vi test.txt 6 cat .cshrc analyze% !3 pwd /disk01/users/abel analyze%

35. UNIX Help

36. analyze% man command • man • Look for a manual entry • man "commnd" • Type in the name of some command • To scroll • Hit the space bar to scroll by page • Hit return to scroll one line at a time • man -k word • Does the term "word" appear in the description for any command?

37. analyze% man ls User Commands ls(1) NAME ls - list contents of directory SYNOPSIS /usr/bin/ls [ -aAbcCdfFgilLmnopqrRstux1 ] [ file ... ] /usr/xpg4/bin/ls [ -aAbcCdfFgilLmnopqrRstux1 ] [ file ... ] DESCRIPTION For each file that is a directory, ls lists the contents of the directory; for each file that is an ordinary file, ls repeats its name and any other information requested. The output is sorted alphabetically by default. When no argument is given, the current directory is listed. When several arguments are given, the arguments are first sorted appropriately, but file arguments appear before directories and their contents.

38. OPTIONS The following options are supported: -a Lists all entries, including those that begin with a dot (.), which are normally not listed. -A Lists all entries, including those that begin with a dot (.), with the exception of the working directory (.) and the parent directory (..). -b Forces printing of non-printable characters to be in the octal \ddd notation. -c Uses time of last modification of the i-node (file created, mode changed, and so forth) for sorting (-t) or printing (-l or -n). -C Multi-column output with entries sorted down the columns. This is the default output format. -d If an argument is a directory, lists only its name (not its contents); often used with -l to get the status of a directory.

39. Files and Directories

40. File Specifications • A place to store information • File names • Lets a program know where to look for the appropriate information • /disk01/users/lefkowit/users/vsvcg.seq • The file vsvcg.seq contains the nucleotide sequence for vesicular stomatitis virus.

41. File Names • Computer doesn’t much care • Differentiates files • Important for us humans • Allows you to remember what the heck is in that file • Make it easy to type • Be careful with spaces and other “weird” characters

42. Naming Files • Most files can be given any name. • Use the complete file name when running a program • Use a name other people can recognize

43. Valid Names or Extensions • Can be 255 characters long • Cannot use a slash / • pathname separator • Can use almost anything else • Names are case sensitive • It is a bad idea to use certain characters: • * • wildcard • tabs, spaces, control characters • invisible

44. Case • Two different files • Brown • brown • Both can exist in the same directory

45. File Names: name.ext • Name should contain specific information describing the file • Sequence name • Figure name • Text file name • ext • File name extension • Not required but helpful

46. Extensions • Indicates the type of file • .txt - text • .com - command • .seq - GCG-formatted nucleotide sequence • .fas – fasta-formatted sequence • .pep - peptide sequence • .pair - Gap or BestFit output

47. Extensions • In the end, it is just part of the overall name • The computer does not do anything special that depends on the extension • my.sequence..is.located.here.seq • This is a completely valid name

48. Files/Directories with the same name • UNIX computers will OVERWRITE and DELETE an existing file if you create or save a new file or directory with the same name!

49. Directories • A place to store things • Files • Other directories

50. Directory Specifications • /disk01/users/lefkowit/seqs/ • disk drive: disk01 • Actually just like any other directory • subdirectory seqs in subdirectory lefkowit in subdirectory users • lefkowit is my login directory