Exons:
Relevant bits of information for using the MUSC Shared Resource,
 the BioMolecular Computing Resource (BCR).

        Exon_7: Some Simple UNIX Commands:

-FTP: invokes Internet file transfer protocol; very, very fast! 
-Telnet: allows remote machine login (for account holders or 
anonymous users). 
*These two commands require that software exist on both machines, 
ie the client and the server (or other remote server).


*At the SGI prompt 'trex or erg or vrap %'. Note the ":" is NOT part 
of the command!

>mkdir directoryname: creates a new directory with the indicated 
name eg:

	%mkdir /home/fuddep/project1  

This allows you to organize your directory in meaningful ways eg 
according to project name etc. 

>rmdir directoryname: removes the indicated directory eg:

	%rmdir /home/fuddep/project1 
 
"project1" directory is removed.

>cd the UNIX change directory command. Examples

	%cd ..: changes from the current directory up one path level; 
thats c, d, space, dot, dot.
	%cd :changes  to the user's root directory; that's c,d,space.
	%cd /home/fuddep/project1/: selects a subdirectory.
	%up: moves up one directory
	%down directoryname: moves down to the indicated directory

	%rm filename: removes the file indicated by ,<filename>

>ls:  (el es; not eye es) the SGI equivalent of the VAX DIR command. 
ls  'lists' the files in your SGI account.
	%ls -a : lists all files including the "." dot files
	%ls -l: lists all files in long format which includes the protection
 for each  file.
	%ls -cp: lists all files but places a "/"  after all directory names.

>pwd: print the working directory.

	%pwd

	%man -k keyword: searches for online help relevant to the keyword.

	%who: same as for VAX also try "who am i" and" w"

	%pine: starts the UNIX mail system.
	
	%more: similar to the VAX "TYPE" command except it advances 
page at  a time. Entering "q"  will stop the scrolling  of long files.

	%cat: displays the contents of a file without stopping at page breaks.
Equivalent to VAX "TYPE" command.

>vi: starts the notorious UNIX editor VI. ":" then "q" exits. See Exon_8.

>pico: starts another UNIX editor.


	%logout: ends your current session.

        
**NOTE: GCG command lines on the VAX had arguments separated by 
slash marks "/" eg.

PILEUP/BATCH/FIGURE=My.Tree/OUTfile=My.MSF

**On the SGI the same  command line arguments are separated by space,
 then dash " -" eg.

pileup -batch -figure=my.tree -outfile=my.msf

**NOTE as well that the SGI line uses lower case characters! Also 
aliases must be defined for the IRIX (UNIX) operating system. For 
example, to execute the GCG program HELICALWHEEL interactively 
on the VAX you would minimally type: 

    HELICAL

On the SGI the same command would have to be:

  helicalwheel