Introduction to GCG & Introduction to GCG & UNIXUNIX

Jianping JinJianping Jin Ph. D.Ph. D.

Center for Bioinformatics Center for Bioinformatics University of North Carolina University of North Carolina

At Chapel HillAt Chapel HillTel: (919)843-6105Tel: (919)843-6105

E-Mail: jjin@unc.eduE-Mail: jjin@unc.edu

Logging on to a UNIX ServerLogging on to a UNIX Server

Must have an approved account: Must have an approved account: user_name + password.user_name + password.

Connect to the server over the network Connect to the server over the network through SSH Secure Shell, Secure CRT?. through SSH Secure Shell, Secure CRT?.

Terminate a session: exit or Terminate a session: exit or File/Disconnect. File/Disconnect.

SSH Secure ShellSSH Secure Shell

A program that provides a secure channel A program that provides a secure channel for network services over an insecure for network services over an insecure network. network. X11 connections and arbitrary TCP/IP X11 connections and arbitrary TCP/IP ports can also be forwarded over the ports can also be forwarded over the secured network.secured network.Insecure terminal applications, such as Insecure terminal applications, such as Telnet and FTP were replaced by SSH Telnet and FTP were replaced by SSH secure shell in connection to the server. secure shell in connection to the server.

SSH for PC UsersSSH for PC Users

X11 for Mac OSX11 for Mac OS

XFree86 (XDarwin): a free implementation XFree86 (XDarwin): a free implementation of the X Window System (X11). For Mac of the X Window System (X11). For Mac OS 10.2.x.OS 10.2.x.

MacSSH or MacSFTP for Mac OS 9 or MacSSH or MacSFTP for Mac OS 9 or earlier.earlier.

Mac OS 10.3 (Panther) incorporated X11, Mac OS 10.3 (Panther) incorporated X11, use the customize installationuse the customize installation

X11 for Mac OS XX11 for Mac OS X

Connection to Server from MacConnection to Server from Mac

Data Transfer for MacData Transfer for Mac

Working with DirectoriesWorking with Directories

Andrew (Network) file system: AFSAndrew (Network) file system: AFSCreate a directory, by issuing the following Create a directory, by issuing the following command: $mkdir directoryNamecommand: $mkdir directoryNameYou can not have spaces in the name.You can not have spaces in the name.Avoid any non-alphanumeric characters.Avoid any non-alphanumeric characters.Directory list: ls, ls –l , ls -alDirectory list: ls, ls –l , ls -alChange directory: cd, cd ..; cd ../..Change directory: cd, cd ..; cd ../..Delete empty directory: rmdirDelete empty directory: rmdirShow current directory: pwdShow current directory: pwd

Working with FilesWorking with Files

Display a file: more, cat Display a file: more, cat (display/combine/append files)(display/combine/append files)

Cancel the file listing: q/ctrl-cCancel the file listing: q/ctrl-c

Moves or renames file(s)/directory(ies): mvMoves or renames file(s)/directory(ies): mv

Delete files: rm, never “rm *”, better “rm –i Delete files: rm, never “rm *”, better “rm –i filename” for prompting before deletion. filename” for prompting before deletion.

Edit a file: vi, pico, ne Edit a file: vi, pico, ne

How GCG works (1)How GCG works (1)

Your input file(s): sequences or output Your input file(s): sequences or output file(s) from a upstream program.file(s) from a upstream program.

Data files: non-sequence info. required for Data files: non-sequence info. required for analyses. analyses.

Define parameters, an output file name Define parameters, an output file name and/or database for running a program.and/or database for running a program.

Run a program by command-line or X-Run a program by command-line or X-WindowsWindows

Command LineCommand Line

Make sure GCG been initialized. “gcg”.Make sure GCG been initialized. “gcg”.

Type the name of the program on the command Type the name of the program on the command line & press enter. Then answer program line & press enter. Then answer program prompts. prompts.

A program name + parameters to customize the A program name + parameters to customize the analysis. –CHEck (for advanced users). analysis. –CHEck (for advanced users).

Running programs in the background (not Running programs in the background (not necessarily, you can open another window necessarily, you can open another window through SSH client). through SSH client).

Getting Help Getting Help

GCG Wisconsin Package Manuals on the GCG Wisconsin Package Manuals on the local web: local web: http://www.unc.edu/gcghttp://www.unc.edu/gcg

Online help: $genhelp, $genmanualOnline help: $genhelp, $genmanual

Technical support: Technical support: jjin@unc.edujjin@unc.edu or 919- or 919-843-6105843-6105

Or Technical support from accelrys, Or Technical support from accelrys, http://www.acceryls.com/support/bio/genhhttp://www.acceryls.com/support/bio/genhelpelp

Using Online HelpUsing Online Help

Genhelp: help organized alphabetically by Genhelp: help organized alphabetically by program name, $genhelpprogram name, $genhelp

Gene Manual: help organized by function, Gene Manual: help organized by function, $genmanual. Each functional category, includes $genmanual. Each functional category, includes the programs and their descriptions the programs and their descriptions

On line for UNIX OS commands: $man On line for UNIX OS commands: $man command_name, e.g. $man ls. Or command_name, e.g. $man ls. Or https://bioinformatics.unc.edu/support/general.hthttps://bioinformatics.unc.edu/support/general.htmm

Running GCG programsRunning GCG programs

Search Database: stringsearch, adh Search Database: stringsearch, adh mRNA; stringsearch, UniProt, adh1/nadh1.mRNA; stringsearch, UniProt, adh1/nadh1.Get the sequence(s) of interests by fetch Get the sequence(s) of interests by fetch (e.g. just use genbank accession number (e.g. just use genbank accession number for individual file(s) or @listfile for multiple for individual file(s) or @listfile for multiple sequences).sequences).Align sequences with pileup. In most Align sequences with pileup. In most cases edition of the searched file is cases edition of the searched file is required (by pico or vi).required (by pico or vi).

SeqlabSeqlab

Open Seqlab interface via X-Windows (see “how Open Seqlab interface via X-Windows (see “how do I get an XWindow service” in do I get an XWindow service” in http://bioinformatics.unc.edu/software/gcg/gcg_fhttp://bioinformatics.unc.edu/software/gcg/gcg_faq.htm#seqlab) .aq.htm#seqlab) .Make a new list: by File/Add Sequences From/. Make a new list: by File/Add Sequences From/. Or Open list: If there has been one.Or Open list: If there has been one.Run multiple alignment by selecting Run multiple alignment by selecting Funtions/Multiple comparison/ and add the Funtions/Multiple comparison/ and add the resulting .msf to the Main listresulting .msf to the Main listSave the list. The list is in your home directory.Save the list. The list is in your home directory.mv the list to the folder where you want it to be.mv the list to the folder where you want it to be.

Printing from GCG (I)Printing from GCG (I)

Define your printer to the GCG server by Define your printer to the GCG server by sending an email to sending an email to research@unc.eduresearch@unc.edu with the printer information. with the printer information.

Details needed: Details needed:

printer type: i.e. HP 7550printer type: i.e. HP 7550

printer IP address: i.e. 152.2.45.54printer IP address: i.e. 152.2.45.54

short description: Bioinfo., Rm 3133short description: Bioinfo., Rm 3133

Printing from GCG (II)Printing from GCG (II)

From the From the command line: command line: <setplot><setplot>GCG will provide GCG will provide a menu from a menu from which user can which user can select a printer. select a printer.

+-------------------> displaying 1 thru 12 of 38 options <------++-------------------> displaying 1 thru 12 of 38 options <------+|ps236h101X HP4 in pmbb (copy) |ps236h101X HP4 in pmbb (copy) |||Mike_Mears Hp 5 M in 106 Glaxo (copy) (copy) |Mike_Mears Hp 5 M in 106 Glaxo (copy) (copy) |||ps236h106X Hp 5 M in 106 Glaxo (copy) (copy) |ps236h106X Hp 5 M in 106 Glaxo (copy) (copy) |||bioinfocol color printer at UNC Bioinfo Center |bioinfocol color printer at UNC Bioinfo Center |||lp170 lp170: 4200n Rm 713 |lp170 lp170: 4200n Rm 713 |||ps206h375 ps206h375: HP 4 in 375 MSRB |ps206h375 ps206h375: HP 4 in 375 MSRB |||peds0199 peds0199: HP 4500N MSRB 377 |peds0199 peds0199: HP 4500N MSRB 377 |||ps236h106 ps236h106: Hp 5 M in 106 Glaxo |ps236h106 ps236h106: Hp 5 M in 106 Glaxo |||ps236h101 ps236h101: HP4 in pmbb |ps236h101 ps236h101: HP4 in pmbb |||ocis32132 ocis32132: 311 dental research center |ocis32132 ocis32132: 311 dental research center |||ps217h414 ps217h414: Hp 4 414 Taylor |ps217h414 ps217h414: Hp 4 414 Taylor ||+---------------------------------------------------------------------------++---------------------------------------------------------------------------+Enter a command. Choices are:Enter a command. Choices are: <up-arrow> and <down-arrow> scroll the list<up-arrow> and <down-arrow> scroll the list <return> makes GCG use the selected device<return> makes GCG use the selected device Q quits without doing anythingQ quits without doing anything

C creates and edits a new deviceC creates and edits a new device D deletes the selectionD deletes the selection|ps236h106 Hp 5 M in 106 Glaxo (copy) |ps236h106 Hp 5 M in 106 Glaxo (copy)

E edits the selectionE edits the selection

Printing from GCG (III)Printing from GCG (III)+-------------------> displaying 1 thru 12 of 38 options <---------------------------++-------------------> displaying 1 thru 12 of 38 options <---------------------------+|ps236h106 Hp 5 M in 106 Glaxo (copy) |ps236h106 Hp 5 M in 106 Glaxo (copy) |||ps236h101X HP4 in pmbb (copy) |ps236h101X HP4 in pmbb (copy) |||Mike_Mears Hp 5 M in 106 Glaxo (copy) (copy) |Mike_Mears Hp 5 M in 106 Glaxo (copy) (copy) |||ps236h106X Hp 5 M in 106 Glaxo (copy) (copy) |ps236h106X Hp 5 M in 106 Glaxo (copy) (copy) |||bioinfocol color printer at UNC Bioinfo Center |bioinfocol color printer at UNC Bioinfo Center |||lp170 lp170: 4200n Rm 713 |lp170 lp170: 4200n Rm 713 |||ps206h375 ps206h375: HP 4 in 375 MSRB |ps206h375 ps206h375: HP 4 in 375 MSRB |||peds0199 peds0199: HP 4500N MSRB 377 |peds0199 peds0199: HP 4500N MSRB 377 |||ps236h106 ps236h106: Hp 5 M in 106 Glaxo |ps236h106 ps236h106: Hp 5 M in 106 Glaxo |||ps236h101 ps236h101: HP4 in pmbb|ps236h101 ps236h101: HP4 in pmbb |||ocis32132 ocis32132: 311 dental research center |ocis32132 ocis32132: 311 dental research center |||ps217h414 ps217h414: Hp 4 414 Taylor |ps217h414 ps217h414: Hp 4 414 Taylor ||+--------------------------------------------------------------------------------------------------++--------------------------------------------------------------------------------------------------+Enter a command. Choices are:Enter a command. Choices are: <up-arrow> and <down-arrow> scroll the list<up-arrow> and <down-arrow> scroll the list <return> makes GCG use the selected device<return> makes GCG use the selected device Q quits without doing anythingQ quits without doing anything

C creates and edits a new deviceC creates and edits a new device (you can't delete from the site file)(you can't delete from the site file) V views the selection (use C to edit a copy)V views the selection (use C to edit a copy)

DoneDone

Plotting Configuration set to: Plotting Configuration set to: Language: psd Language: psd Device: LASERWRITERDevice: LASERWRITER Port or Queue: | lp -c -d ps236h101Port or Queue: | lp -c -d ps236h101

Select a printer and Select a printer and press return.press return.

Plotting Plotting configuration configuration shows the shows the settings: i.e. settings: i.e. Language, Language, device and the device and the printting queue. printting queue.

Printing from GCG (IV)Printing from GCG (IV)

Select a printer Select a printer and press return.and press return.Configuration Configuration shows Language, shows Language, Device and Device and printing Queue.printing Queue.

$ setplot$ setplot

SETPLOT allows you to choose a plotting configuration from a menu ofSETPLOT allows you to choose a plotting configuration from a menu ofavailable graphics devices at your site.available graphics devices at your site.+-------------------> displaying 1 thru 12 of 38 options <---------------------------++-------------------> displaying 1 thru 12 of 38 options <---------------------------+|ps236h106 Hp 5 M in 106 Glaxo (copy) |ps236h106 Hp 5 M in 106 Glaxo (copy) |||ps236h101X HP4 in pmbb (copy)|ps236h101X HP4 in pmbb (copy) |||Mike_Mears Hp 5 M in 106 Glaxo (copy) (copy) |Mike_Mears Hp 5 M in 106 Glaxo (copy) (copy) |||ps236h106X Hp 5 M in 106 Glaxo (copy) (copy) |ps236h106X Hp 5 M in 106 Glaxo (copy) (copy) |||bioinfocol color printer at UNC Bioinfo Center |bioinfocol color printer at UNC Bioinfo Center |||lp170 lp170: 4200n Rm 713 |lp170 lp170: 4200n Rm 713 |||ps206h375 ps206h375: HP 4 in 375 MSRB |ps206h375 ps206h375: HP 4 in 375 MSRB |||peds0199 peds0199: HP 4500N MSRB 377 |peds0199 peds0199: HP 4500N MSRB 377 |||ps236h106 ps236h106: Hp 5 M in 106 Glaxo |ps236h106 ps236h106: Hp 5 M in 106 Glaxo |||ps236h101 ps236h101: HP4 in pmbb |ps236h101 ps236h101: HP4 in pmbb |||ocis32132 ocis32132: 311 dental research center |ocis32132 ocis32132: 311 dental research center |||ps217h414 ps217h414: Hp 4 414 Taylor |ps217h414 ps217h414: Hp 4 414 Taylor ||+--------------------------------------------------------------------------------------------------++--------------------------------------------------------------------------------------------------+Enter a command. Choices are:Enter a command. Choices are: <up-arrow> and <down-arrow> scroll the list<up-arrow> and <down-arrow> scroll the list <return> makes GCG use the selected device<return> makes GCG use the selected device Q quits without doing anythingQ quits without doing anything

C creates and edits a new deviceC creates and edits a new device D deletes the selectionD deletes the selection E edits the selectionE edits the selection

DoneDone

Plotting Configuration set to: Plotting Configuration set to: Language: hpd Language: hpd Device: LASERJETIIIDevice: LASERJETIII Port or Queue: | lp -c -d ps236h101Port or Queue: | lp -c -d ps236h101

Printing from GCG (V)Printing from GCG (V)

The The file, .gcgmydevices, file, .gcgmydevices, under a user’s home under a user’s home directory describes the directory describes the graphics devices that graphics devices that are available to the are available to the user. user. A user should be able A user should be able to create a local GCG to create a local GCG personal defined personal defined printer by setplot or printer by setplot or edition of edition of the .gcgmydevices the .gcgmydevices file. A global printer file. A global printer setting should be done setting should be done by a system by a system administrator administrator (sitedevices.configure)(sitedevices.configure)

$ pwd$ pwd/afs/isis.unc.edu/home/j/j/jjin/afs/isis.unc.edu/home/j/j/jjin$ more .gcgmydevices$ more .gcgmydevices! This file describes GCG graphics devices used only by you.! This file describes GCG graphics devices used only by you.! You can edit it by hand, but we recommend using setplot instead,! You can edit it by hand, but we recommend using setplot instead,! or the "Graphics Devices" command on the "Option" menu in SeqLab.! or the "Graphics Devices" command on the "Option" menu in SeqLab.

! Device Configurations! Device Configurations

command: ps236h106 = 'postscript LaserWriter "| lp -c -d ps236h106"'command: ps236h106 = 'postscript LaserWriter "| lp -c -d ps236h106"'description: Hp 5 M in 106 Glaxo (copy)description: Hp 5 M in 106 Glaxo (copy)context: setplot seqlabcontext: setplot seqlab

command: ps236h101X = 'hpgl LaserJetIII "| lp -c -d ps236h101"'command: ps236h101X = 'hpgl LaserJetIII "| lp -c -d ps236h101"'description: HP LaserJet 8150 in Ctr for Bioinformaticsdescription: HP LaserJet 8150 in Ctr for Bioinformaticscontext: setplot seqlabcontext: setplot seqlab

command: Mike_Mears = 'postscript LaserWriter "| lp -c -d lp170"'command: Mike_Mears = 'postscript LaserWriter "| lp -c -d lp170"'description: Hp 5 M in 106 Glaxo (copy) (copy)description: Hp 5 M in 106 Glaxo (copy) (copy)context: setplot seqlabcontext: setplot seqlab

command: ps236h106X = 'postscript LaserWriter "| lp -c -d ps236h106"'command: ps236h106X = 'postscript LaserWriter "| lp -c -d ps236h106"'description: Hp 5 M in 106 Glaxo (copy) (copy)description: Hp 5 M in 106 Glaxo (copy) (copy)context: setplot seqlabcontext: setplot seqlab

command: bioinfocol = 'postscript LaserWriter "lp -c -d bioinfocolor" Jet 45command: bioinfocol = 'postscript LaserWriter "lp -c -d bioinfocolor" Jet 4550 "lp -c -d bioinfocolor" Jet 4550 "| lp -c -d bioinfocolor"'50 "lp -c -d bioinfocolor" Jet 4550 "| lp -c -d bioinfocolor"'description: color printer at UNC Bioinfo Centerdescription: color printer at UNC Bioinfo Centercontext: setplot seqlabcontext: setplot seqlab

Printing from Seqlab (text)Printing from Seqlab (text)

Printing from Seqlab (graphics)Printing from Seqlab (graphics)