Using Computers

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Using Computers

• orSlowly going insane

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UNIX

• Rapidly going insane

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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

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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.

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Help!!!

• On analyze
• analyze genhelp
• analyze genmanual
• GCG commands
• analyze man
• UNIX
• Web-based
• Me (Elliot)

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SeqLab Help

• Xwindows interface

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SeqLab Help
8
SeqWeb Help

• gcg.genome.uab.edu

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SeqStore Help

• http//gcg.genome.uab.edu8050/seqstore_cgi/user_h
  ome.cgi

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Elliot Help

• E-mail to ElliotL_at_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

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Logging On

• Telnet to gcg.genome.uab.edu
• Username
• Password
• System Announcements
• Mail Messages

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Logging Out

• Finished. I want to go home.
• analyze logout

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Login Messages

• SunOS 5.8
• login abel
• Password
• Last login Tue Apr 3 111413 from GENWORK0
• Sun Microsystems Inc. SunOS 5.8 Generic
  February 2000
• UAB Molecular and Genetic
  Bioinformatics Facility
• For help contact Elliot
  Lekfowitz
• [phone]
• ELLIOTL_at_uab.edu
• or visit our web site
  http//www.genome.uab.edu/
• MIC753 - Practical Applications of
  Sequence Analysis
• analyze

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Changing your password

• analyze passwd
• analyze passwd
• Changing password for lefkowit.
• Old password
• New password
• Retype new password
• analyze

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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

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.login

• analyze cat .login
• _at_()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

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.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

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Changing your .login file

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

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.cshrc

• analyze cat .cshrc
• _at_()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 history32
• endif
• alias h history
• alias edit /usr/dt/bin/dtpad
• alias acroread /opt/Acrobat4/bin/acroread
  
• alias lo logout
• limit coredumpsize 0

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The Command Prompt

• analyze
• Type your commands following the prompt
• Different UNIX shells use different prompts

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Entering Commands

• Type command at the analyze prompt
• Edit with the delete/backspace key
• Hit Return
• Sends command to the computer

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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

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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

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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

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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

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Long Commands

• analyze map -infilegendocdataggamma.seq data
  \
• enzyme.dat -once -six -cir

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history

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

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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

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UNIX Help
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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?

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• 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

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• 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.

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Files and Directories
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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.

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File Names

• Computer doesnt 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

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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

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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

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Case

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

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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

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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

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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

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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!

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Directories

• A place to store things
• Files
• Other directories

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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

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Login directory

• Generally your username
• lefkowit
• Home Directory
• analyze home
• Takes you home
• GCG command
• analyze cd
• UNIX equivalent

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SubDirectories

• Allows storage of files into different "folders"
• lefkowit/sequence
• lefkowit/sequence/vsv

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Commands
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UNIX Commands

• Type the command name at the analyze prompt
• Follow the name with qualifiers (if any)
• Qualifiers are preceded by a hyphen -
• Multiple qualifiers can be used
• ls -CFal
• Combines the C, F, a, and l qualifier for the ls
  command

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GCG vs. UNIX Commands

• UNIX commands
• cshell commands
• GCG commands
• Specific for the GCG program

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It Doesn't Work!

• UNIX commands
• GCG commands
• up
• down
• Which are which?
• UNIX commands are listed in the man pages
• analyze man down
• analyze man down
• No manual entry for down.
• analyze

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Control Keys

• Press control and the indicated key
  simultaneously
• Provides control of various computer functions

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Abort Program

• ctrl-c
• Aborts program execution

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UNIX Commands

• Directory Listings

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ls

• Directory listing
• analyze ls
• List the files in the current directory.
• analyze ls sequence
• List all the files in the sequence subdirectory

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analyze ls 8_Recommended.zip gcgrdb
pox admin
license_WS5 ppc AdobeFnt.lst
Mail solregis.old anonftp.
setup mbox
spl Auburn_012001_final.ppt mh
src chha_homam.sw mic753
strep chha_homam.tfa
mih_calsi.tfa tmp DeadLetters
ns_imap TTauthority.old dell.
pdf nsmail
users dt.old oberon
working.list DttermLogkGG.H
oracle Xauthority.old gcg
patch gcgff
paup analyze
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ls...

• analyze ls paup
• List all files in the subirectory paup
• analyze ls paup/ AND all files in
  subdirectories one level below paup

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analyze ls paup get_paup
paup4b8-sparc_ultra64 paup4b7-sparc_ultra64
paup4b8-sparc_ultra64.tar analyze ls
paup/ paup/get_paup
paup/paup4b8-sparc_ultra64.tar
paup/paup4b7-sparc_ultra64 Docs
Release-Notes.txt Sample_import_data README
Sample_analysis_files
Sample_NEXUS_data paup/paup4b8-sparc_ultra64 Do
cs Release-Notes.txt
Sample_import_data README
Sample_analysis_files Sample_NEXUS_data analyze
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Wild Cards

• Allows ambiguous specifications
• Allows references to multiple files

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Wild Card Specification

• Any character
• Any number of characters
• ?
• Any single character
• Placement important

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Wildcard Usage

• Use with most commands which refer to files
• analyze ls .seq
• Use at GCG program prompts
• Sequence(s)
• Multiple sequences allowed

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Example 1

• mysequence.
• All files named mysequence with any file
  extension
• May refer to both nucleotide and peptide versions
  of mysequence
• .seq
• .pep

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Example 2

• MY
• All files beginning with MY

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Example 3

• .seq
• All nucleotide sequences in the current directory

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ls parameters

• -F
• Subdirectories end in a /
• -a
• Show hidden files
• -l
• long listing
• -t
• sort by time of last modification

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ls

• analyze ls
• 8_Recommended.zip gcgrdb
  pox
• admin license_WS5
  ppc
• AdobeFnt.lst Mail
  solregis.old
• anonftp.setup mbox
  spl
• Auburn_012001_final.ppt mh
  src
• chha_homam.sw mic753
  strep
• chha_homam.tfa mih_calsi.tfa
  tmp
• DeadLetters ns_imap
  TTauthority.old
• dell.pdf nsmail
  users
• dt.old oberon
  working.list
• DttermLogkGG.H oracle
  Xauthority.old
• gcg patch
• gcgff paup

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ls -F

• analyze ls -F
• 8_Recommended.zip gcgrdb
  pox/
• admin/ license_WS5
  ppc/
• AdobeFnt.lst Mail/
  solregis.old/
• anonftp.setup mbox
  spl/
• Auburn_012001_final.ppt mh/
  src/
• chha_homam.sw mic753/
  strep/
• chha_homam.tfa mih_calsi.tfa
  tmp/
• DeadLetters/ ns_imap/
  TTauthority.old
• dell.pdf nsmail/
  users/
• dt.old/ oberon/
  working.list
• DttermLogkGG.H oracle/
  Xauthority.old
• gcg/ patch/
• gcgff paup/

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ls -a

• analyze ls -a
• . .seqlab-history
  Mail
• .. .solregis
  mbox
• .acrorc .ssh2
  mh
• .acrosrch .tt
  mic753
• .bash_history .TTauthority
  mih_calsi.tfa
• .cetables .vconsole.properties
  ns_imap
• .cshrc .Xauthority
  nsmail
• .desksetdefaults 8_Recommended.zip
  oberon
• .dt admin
  oracle
• .dtprofile AdobeFnt.lst
  patch
• .eserve-options anonftp.setup
  paup
• .gcgmydevices Auburn_012001_final.ppt
  pox
• .License_Request_Form chha_homam.sw
  ppc
• .login chha_homam.tfa
  solregis.old
• .mailcap DeadLetters
  spl
• .mailrc dell.pdf
  src
• .ncbirc dt.old
  strep
• .netscape DttermLogkGG.H
  tmp

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ls -l
analyze ls -l total 34318 -rw-r--r-- 1
lefkowit staff 14513574 Oct 17 1522
8_Recommended.zip drwxr-xr-x 4 lefkowit staff
512 Aug 7 2000 admin -rw-rw-rw- 1
lefkowit staff 22016 Jul 3 2000
AdobeFnt.lst -rwxr--r-- 1 lefkowit staff
5284 Jan 5 1417 anonftp.setup -rw-r--r-- 1
lefkowit staff 2299904 Jan 24 1645
Auburn_012001_final.ppt -rw-r--r-- 1 lefkowit
staff 5243 Jan 22 1429 chha_homam.sw -rw-r-
-r-- 1 lefkowit staff 199 Jan 22 1429
chha_homam.tfa drwx------ 2 lefkowit staff
512 Nov 28 1605 DeadLetters -rw-r--r-- 1
lefkowit staff 650650 Sep 15 2000
dell.pdf drwxr-xr-x 12 lefkowit staff 512
Apr 2 1055 dt.old -rw-r--r-- 1 lefkowit staff
104 Aug 14 2000 DttermLogkGG.H drwxr-xr-x
2 lefkowit staff 512 Jul 10 2000
gcg -rw-r--r-- 1 lefkowit staff 34 Sep
15 2000 gcgff -rw-r--r-- 1 lefkowit staff
391 Sep 27 2000 gcgrdb
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Long Listing

• -rw-r--r-- 1 lefkowit staff 650650 Sep 15
  2000 dell.pdf
• file type and permissions -rw-r--r--
• type (- or d) - for a regular file d for a
  directory
• (r, w, x) read, write, execute, permissions (-
  for none)
• owner, group, everyone
• file links 1
• owner id lefkowit
• group id sequence
• size in bytes 650650
• time stamp (last modified) Sep 15, 2000
• name dell.pdf

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pwd

• Where am I?
• print working directory
• analyze pwd
• /disk01/users/lefkowit/users/uugen
• analyze

77
Working Directory

• All action occurs here
• Unless you specify a different directory

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up

• Go to the directory one up from my current
  directory
• GCG command

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down

• down DirectoryName
• analyze down sequences
• Go down to the sequences directory
• GCG Command

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cd

• Change your working directory
• analyze cd sequences
• go down to sequences
• analyze cd sequences/vsv
• go down to the directory vsv that is in the
  directory sequences

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..

• A double period refers to the directory directly
  above where you are currently located.

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.. Examples

• cd ..
• Take me up one directory level
• cd ../..
• Take me up two directory levels
• cd ../proteins
• Go up one level and then from there, down to the
  directory proteins

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.

• One period refers to the current directory

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home

• Take me to my login directory
• GCG command

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mkdir name

• Make directory
• Creates a subdirectory in the current directory
• analyze mkdir homework
• Creates a new subdirectory with the name homework

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rmdir name

• Remove directory
• Deletes a subdirectory
• First delete all files within the subdirectory

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UNIX Commands

• File manipulation

88
cp filename1 filename2

• Creates a copy of a file or directory with a new
  name
• cp elliot george
• make a duplicate copy of the file elliot and call
  it george
• cp elliot men/elliot
• make a copy of the file elliot call it elliot
  and put it in the subdirectory men

89
rm filename

• Removes (deletes) a file

90
mv filename1 filename2

• Changes a file or directory name
• Moves a file to a different directory
• mv elliot george
• Change the name of the file elliot to george
• mv elliot men/elliot
• moves the file elliot into the subdirectory men

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more filename

• List the contents of a file to the screen one
  page at a time
• Use the space bar to scroll
• analyze more .login

92
cat filename

• List the contents of the file to the screen
• Does not pause between pages

93
grep pattern filename(s)

• Find all occurrences of a text pattern in a
  file(s)

94
grep
analyze ls -a . .login
.seqlab-history test.txt ..
.profile .ssh2 .cshrc
.seqlab-analyze .Xauthority analyze grep alias
. .cshrcalias h history .cshrcalias
edit /usr/dt/bin/dtpad .cshrcalias
acroread /opt/Acrobat4/bin/acroread .cshrc
alias lo logout analyze grep alias
analyze
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Is that program still running?

• process status
• analyze ps
• Show me my processes
• analyze ps -ef
• Show me all processes

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ps
analyze ps PID TTY TIME CMD 17422 pts/8
000 csh analyze ps -ef UID PID PPID
C STIME TTY TIME CMD root 0 0
0 Mar 08 ? 003 sched root 1
0 0 Mar 08 ? 025 /etc/init - root
2 0 0 Mar 08 ? 000 pageout
root 3 0 1 Mar 08 ? 136546
fsflush root 1599 1 0 Mar 08 ?
000 /usr/lib/saf/sac -t 300 root 1363 1
0 Mar 08 ? 001 /usr/sbin/syslogd
97
Redirecting Input and Output

• command lt filename
• the contents of the file filename is used as
  input to the command preceding the lt
• command gt filename
• The output from command is sent to the file
  filename

98
Redirecting Output

• analyze ls -a
• . .login .seqlab-history
  test.txt
• .. .profile .ssh2
• .cshrc .seqlab-analyze .Xauthority
• analyze ls -a gt list
• analyze cat list
• .
• ..
• .cshrc
• .login
• .profile
• .seqlab-analyze
• .seqlab-history
• .ssh2
• .Xauthority
• list
• test.txt
• analyze

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The Pipe

• command1 command2
• is called a pipe character
• directs the output of command1 to be used as
  input for command2

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analyze ps -ef grep lefkowit

• analyze ps -ef grep oracle
• abel 19835 17422 0 140927 pts/8 000
  grep oracle
• oracle 6192 1 0 Mar 29 ? 000
  ora_reco_seqstore
• oracle 6190 1 0 Mar 29 ? 003
  ora_smon_seqstore
• oracle 6186 1 0 Mar 29 ? 135
  ora_lgwr_seqstore
• oracle 6205 1 0 Mar 29 ? 000
  /disk00/app/oracle/product/8.0.6t
• oracle 6184 1 0 Mar 29 ? 235
  ora_dbw0_seqstore
• oracle 6182 1 0 Mar 29 ? 000
  ora_pmon_seqstore
• oracle 6188 1 0 Mar 29 ? 140
  ora_ckpt_seqstore
• oracle 6390 6389 0 Mar 29 ? 000
  oracleseqstore (DESCRIPTION(LOC)
• oracle 6369 6367 0 Mar 29 ? 000
  oracleseqstore (DESCRIPTION(LOC)
• analyze

101
Editing

• Text Files
• NOT sequence files!
• Use GCG's sequence editing tools

102
Editing Text Files

• Text-terminal based editor on oberon
• vi
• Xwindows based editor on oberon
• /usr/dt/bin/dtpad
• Your Mac or PC
• Transfer the file from analyze using FTP
• Edit with Word or some other editor
• Save as a text file
• Transfer back to analyze

103
Mail

• Your Email address on analyze is
• username_at_analyze.genome.uab.edu
• Use your current Email account
• Forward mail from analyze to this account
• Create a .forward file
• analyze cat .forward
• elliotl_at_uab.edu
• analyze

104
Using XWindows

• Install X-Win32
• Configure X-Win32
• Command to run
• nohup /usr/dt/bin/dtterm -display MYIP0 -ls

105
Next up...

• Using GCG