Using Analyze

Using Analyze
(and other UNIX computers)

Logging On

Telnet to gcg.genome.uab.edu

For Xwindows run the program:
/usr/dt//bin/dtterm -ls

Command-line Syntax

analyze% command -PARameter

"analyze%" is the command prompt. Type your commands following this prompt

Use at least one space between the command and its parameters

Commands are case sensitive (use lower case)

Do not abbreviate command names

Line editing commands

Delete (or Backspace) Key

Delete the character to the left of the cursor

Long Commands

At the end of the line type a backslash (\) and hit return

To Replay a previous command

analyze% history
Shows you the commands you have previously issued
To replay command number 5 type an exclamation point and the number 5:
analyze% !5

Help

analyze% man command_name

Displays online documentation about the command

analyze% man -k list

Displays all commands that relate to the word list

File and Directory Specifications

Directory names and file names are case sensitive

Directory names (and file names) are separated with a forward slash (/)

/disk01/users/lefkowit/seqs/vsvcg.seq

Names can be pretty much anything

Files with the same name will be overwritten!

Wild Cards

* Any number of any character;

? Any single character

Control Keys

ctrl-c ends a program

ctrl-d end of file

UNIX Commands

General

logout

Finished. I want to go home.

passwd

Change your password

Directory Manipulation

ls

List the files in the current directory.

analyze% ls seqs

List files in the subdirectory named seqs

analyze% ls seqs*

List all files that begin with the letters seq

ls -lt

provides more file information and sorts the listing by date

cd directory_name

Change to the directory_name directory

pwd

Where am I?

. (single period)

refers to the current directory

.. (double period)

refers to the directory directly above the current one

cd ..

Go up one directory

up (GCG Command)

Go to the directory one up from my current directory

down directory_name (GCG Command)

Go down to the directory_name directory

home (or type just cd)

Take me to my login directory

mkdir directory_name

Creates a new subdirectory in the current directory

rmdir directory_name

deletes a directory

File Handling

cp filename1 filename2

Create a copy of a filename1 (and call it filename2)

rm filename

Deletes a file

mv filename1 filename2

Changes the file name

grep 'character_pattern' filename(s)

find the lines in filename(s) that match the pattern

Text Output

cat filename

List the file to the screen

more filename

List the file to the screen one page at a time

	Telnet to gcg.genome.uab.edu
	For Xwindows run the program: /usr/dt//bin/dtterm -ls

	"analyze%" is the command prompt. Type your commands following this prompt
	Use at least one space between the command and its parameters
	Commands are case sensitive (use lower case)
	Do not abbreviate command names

	Directory names and file names are case sensitive
	Directory names (and file names) are separated with a forward slash (/)

Using Analyze (and other UNIX computers)

UNIX Commands

Using Analyze
(and other UNIX computers)