Introduction to GCG & UNIX

1. Introduction to GCG & UNIX Jianping JinPh. D. Center for Bioinformatics University of North Carolina At Chapel Hill Tel: (919)843-6105 E-Mail: jjin@unc.edu

2. 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.

3. 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.

4. SSH for PC Users

5. 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

6. X11 for Mac OS X

7. Connection to Server from Mac

8. Data Transfer for Mac

9. 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

10. 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

11. 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 X-Windows

12. 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).

13. Getting Help • GCG Wisconsin Package Manuals on the local web: http://www.unc.edu/gcg • Online help: $genhelp, $genmanual • Technical support: jjin@unc.edu or 919-843-6105 • Or Technical support from accelrys, http://www.acceryls.com/support/bio/genhelp

14. 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.htm

15. 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).

16. Seqlab • Open Seqlab interface via X-Windows (see “how do I get an XWindow service” in http://bioinformatics.unc.edu/software/gcg/gcg_faq.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.

17. Printing from GCG (I) • Define your printer to the GCG server by sending an email to research@unc.edu 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

18. 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 (II)

19. +-------------------> 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 Select a printer and press return. Plotting configuration shows the settings: i.e. Language, device and the printting queue. Printing from GCG (III)

20. 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 (IV)

21. 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 GCG (V)

22. Printing from Seqlab (text)

23. Printing from Seqlab (graphics)