Transcript SSH for PC Users - UNC Center for Bioinformatics

Introduction to GCG & UNIX
Jianping Jin Ph. D.
Center for Bioinformatics
University of North Carolina
At Chapel Hill
Tel: (919)843-6105
E-Mail: [email protected]
Logging on to a UNIX Server
Must have an approved account:
user_name + password.
Connect to the server over the network
through SSH Secure Shell, Secure CRT?.
Terminate a session: exit or
File/Disconnect.
SSH Secure Shell
A program that provides a secure channel
for network services over an insecure
network.
X11 connections and arbitrary TCP/IP
ports can also be forwarded over the
secured network.
Insecure terminal applications, such as
Telnet and FTP were replaced by SSH
secure shell in connection to the server.
SSH for PC Users
X11 for Mac OS
XFree86 (XDarwin): a free implementation
of the X Window System (X11). For Mac
OS 10.2.x.
MacSSH or MacSFTP for Mac OS 9 or
earlier.
Mac OS 10.3 (Panther) incorporated X11,
use the customize installation
X11 for Mac OS X
Connection to Server from Mac
Data Transfer for Mac
Working with Directories
Andrew (Network) file system: AFS
Create a directory, by issuing the following
command: $mkdir directoryName
You can not have spaces in the name.
Avoid any non-alphanumeric characters.
Directory list: ls, ls –l , ls -al
Change directory: cd, cd ..; cd ../..
Delete empty directory: rmdir
Show current directory: pwd
Working with Files
Display a file: more, cat
(display/combine/append files)
Cancel the file listing: q/ctrl-c
Moves or renames file(s)/directory(ies): mv
Delete files: rm, never “rm *”, better “rm –i
filename” for prompting before deletion.
Edit a file: vi, pico, ne
How GCG works (1)
Your input file(s): sequences or output
file(s) from a upstream program.
Data files: non-sequence info. required for
analyses.
Define parameters, an output file name
and/or database for running a program.
Run a program by command-line or XWindows
Command Line
Make sure GCG been initialized. “gcg”.
Type the name of the program on the command
line & press enter. Then answer program
prompts.
A program name + parameters to customize the
analysis. –CHEck (for advanced users).
Running programs in the background (not
necessarily, you can open another window
through SSH client).
Getting Help
GCG Wisconsin Package Manuals on the
local web: http://www.unc.edu/gcg
Online help: $genhelp, $genmanual
Technical support: [email protected] or 919843-6105
Or Technical support from accelrys,
http://www.acceryls.com/support/bio/genh
elp
Using Online Help
Genhelp: help organized alphabetically by
program name, $genhelp
Gene Manual: help organized by function,
$genmanual. Each functional category, includes
the programs and their descriptions
On line for UNIX OS commands: $man
command_name, e.g. $man ls. Or
https://bioinformatics.unc.edu/support/general.ht
m
Running GCG programs
Search Database: stringsearch, adh
mRNA; stringsearch, UniProt, adh1/nadh1.
Get the sequence(s) of interests by fetch
(e.g. just use genbank accession number
for individual file(s) or @listfile for multiple
sequences).
Align sequences with pileup. In most
cases edition of the searched file is
required (by pico or vi).
Seqlab
Open Seqlab interface via X-Windows (see “how
do I get an XWindow service” in
http://bioinformatics.unc.edu/software/gcg/gcg_f
aq.htm#seqlab) .
Make a new list: by File/Add Sequences From/.
Or Open list: If there has been one.
Run multiple alignment by selecting
Funtions/Multiple comparison/ and add the
resulting .msf to the Main list
Save the list. The list is in your home directory.
mv the list to the folder where you want it to be.
Printing from GCG (I)
Define your printer to the GCG server by
sending an email to [email protected]
with the printer information.
Details needed:
printer type: i.e. HP 7550
printer IP address: i.e. 152.2.45.54
short description: Bioinfo., Rm 3133
Printing from GCG (II)
From the
command line:
<setplot>
GCG will provide
a menu from
which user can
select a printer.
+-------------------> displaying 1 thru 12 of 38 options <------+
|ps236h101X HP4 in pmbb (copy)
|
|Mike_Mears Hp 5 M in 106 Glaxo (copy) (copy)
|
|ps236h106X Hp 5 M in 106 Glaxo (copy) (copy)
|
|bioinfocol color printer at UNC Bioinfo Center
|
|lp170
lp170: 4200n Rm 713
|
|ps206h375 ps206h375: HP 4 in 375 MSRB
|
|peds0199 peds0199: HP 4500N MSRB 377
|
|ps236h106 ps236h106: Hp 5 M in 106 Glaxo
|
|ps236h101 ps236h101: HP4 in pmbb
|
|ocis32132 ocis32132: 311 dental research center
|
|ps217h414 ps217h414: Hp 4 414 Taylor
|
+---------------------------------------------------------------------------+
Enter a command. Choices are:
<up-arrow> and <down-arrow> scroll the list
<return> makes GCG use the selected device
Q quits without doing anything
C creates and edits a new device
D deletes the selection
|ps236h106 Hp 5 M in 106 Glaxo (copy)
E edits the selection
Printing from GCG (III)
Select a printer and
press return.
Plotting
configuration
shows the
settings: i.e.
Language,
device and the
printting queue.
+-------------------> displaying 1 thru 12 of 38 options <---------------------------+
|ps236h106 Hp 5 M in 106 Glaxo (copy)
|
|ps236h101X HP4 in pmbb (copy)
|
|Mike_Mears Hp 5 M in 106 Glaxo (copy) (copy)
|
|ps236h106X Hp 5 M in 106 Glaxo (copy) (copy)
|
|bioinfocol color printer at UNC Bioinfo Center
|
|lp170
lp170: 4200n Rm 713
|
|ps206h375 ps206h375: HP 4 in 375 MSRB
|
|peds0199 peds0199: HP 4500N MSRB 377
|
|ps236h106 ps236h106: Hp 5 M in 106 Glaxo
|
|ps236h101 ps236h101: HP4 in pmbb
|
|ocis32132 ocis32132: 311 dental research center
|
|ps217h414 ps217h414: Hp 4 414 Taylor
|
+--------------------------------------------------------------------------------------------------+
Enter a command. Choices are:
<up-arrow> and <down-arrow> scroll the list
<return> makes GCG use the selected device
Q quits without doing anything
C creates and edits a new device
(you can't delete from the site file)
V views the selection (use C to edit a copy)
Done
Plotting Configuration set to:
Language: psd
Device: LASERWRITER
Port or Queue: | lp -c -d ps236h101
Printing from GCG (IV)
Select a printer
and press return.
Configuration
shows Language,
Device and
printing Queue.
$ setplot
SETPLOT allows you to choose a plotting configuration from a menu of
available graphics devices at your site.
+-------------------> displaying 1 thru 12 of 38 options <---------------------------+
|ps236h106 Hp 5 M in 106 Glaxo (copy)
|
|ps236h101X HP4 in pmbb (copy)
|
|Mike_Mears Hp 5 M in 106 Glaxo (copy) (copy)
|
|ps236h106X Hp 5 M in 106 Glaxo (copy) (copy)
|
|bioinfocol color printer at UNC Bioinfo Center
|
|lp170
lp170: 4200n Rm 713
|
|ps206h375 ps206h375: HP 4 in 375 MSRB
|
|peds0199 peds0199: HP 4500N MSRB 377
|
|ps236h106 ps236h106: Hp 5 M in 106 Glaxo
|
|ps236h101 ps236h101: HP4 in pmbb
|
|ocis32132 ocis32132: 311 dental research center
|
|ps217h414 ps217h414: Hp 4 414 Taylor
|
+--------------------------------------------------------------------------------------------------+
Enter a command. Choices are:
<up-arrow> and <down-arrow> scroll the list
<return> makes GCG use the selected device
Q quits without doing anything
C creates and edits a new device
D deletes the selection
E edits the selection
Done
Plotting Configuration set to:
Language: hpd
Device: LASERJETIII
Port or Queue: | lp -c -d ps236h101
Printing from GCG (V)
The file,
.gcgmydevices, under
a user’s home
directory describes the
graphics devices that
are available to the
user.
A user should be able
to create a local GCG
personal defined
printer by setplot or
edition of the
.gcgmydevices file. A
global printer setting
should be done by a
system administrator
(sitedevices.configure)
$ pwd
/afs/isis.unc.edu/home/j/j/jjin
$ more .gcgmydevices
! This file describes GCG graphics devices used only by you.
! You can edit it by hand, but we recommend using setplot instead,
! or the "Graphics Devices" command on the "Option" menu in SeqLab.
! Device Configurations
command: ps236h106 = 'postscript LaserWriter "| lp -c -d ps236h106"'
description: Hp 5 M in 106 Glaxo (copy)
context: setplot seqlab
command: ps236h101X = 'hpgl LaserJetIII "| lp -c -d ps236h101"'
description: HP LaserJet 8150 in Ctr for Bioinformatics
context: setplot seqlab
command: Mike_Mears = 'postscript LaserWriter "| lp -c -d lp170"'
description: Hp 5 M in 106 Glaxo (copy) (copy)
context: setplot seqlab
command: ps236h106X = 'postscript LaserWriter "| lp -c -d ps236h106"'
description: Hp 5 M in 106 Glaxo (copy) (copy)
context: setplot seqlab
command: bioinfocol = 'postscript LaserWriter "lp -c -d bioinfocolor" Jet 45
50 "lp -c -d bioinfocolor" Jet 4550 "| lp -c -d bioinfocolor"'
description: color printer at UNC Bioinfo Center
context: setplot seqlab
Printing from Seqlab (text)
Printing from Seqlab (graphics)