Using command line programs

Introduction

We expect that most users will be satisfied with the w2h web interface to the GCG and EMBOSS programs. For some "power users" though, the command line is still a requirement. On this page some basics for command line usage are described. The documentation will be improved over time - after the transition from the old machine to the new one has completed.

GCG programs

The GCG programs must be "setup" before they will work correctly. The GCG programs are best supported in the tcsh shell - we do not recommend that you run them from any other shell. To setup GCG enter the following commands:

   # setup gcg
   # setplot         optional - do only if you want to change graphics device
   # genhelp         optional - command line access to documentation
   # gap -infile1=one.seq -infile2=two.seq -endweight
                     GCG on unix uses "-" to delimit command line options
                     One more spaces must precede this symbol.
   # gap -check      All GCG programs will list their arguments this way

EMBOSS programs

The EMBOSS programs do not need to be "setup" before they will work correctly. The EMBOSS programs that produce graphical output go through there own driver. That is, GCG setplot will not affect them. EMBOSS also includes the EMBASSY programs, which are programs which were originally not part of the package but which have been modified so that they can run through the same interface. These include PHYLIP, TOPO, EMNU, and MSE.

   # wossname " "    List all EMBOSS programs, single line descriptions
   # program -help   standard EMBOSS method for showing command line options
   # dottup -sequencea pir:a1hu -sequenceb pir:a1hu -wordsize 2 -graph ps
   Displays a wordmatch dotplot of two sequences
   Created dottup.ps
                     Dotplot a protein against itself and create a postscript file
   # seqret -sequence=pir:a1hu -sbegin=20 -send=30 -outseq=gcg::one.pep
   # seqret -sequence pir:a1hu -sbegin 20 -send 30 -outseq fasta::one.pfa
                     Preceding two commands both extract residues 20-30 from A1hu.
                     The first saves in gcg format, the second in fasta format.

Printing

Use the pdq command to print files. Typical commands:

   
   # pdq -h                              lists all known printers and pdq options
   # lpd_status printername@safserver    jobs queue through slidemaker machine
   # lpd_cancel 5 printername@safserver  stuck job? Cancel it this way
   # man pdq                             figure out the rest yourself!
   

Most other programs

There is no standard for calling other programs. Most have a man page though. Typical commands:

   # man -k progname         Does the program have a man page?            
   # which progname          Does the program exist on your path?            
   # progname -h             Try for run time help (may or may not exist)            
   # progname option option > outfile      
                             Direct output to a file            
   # progname option option >> outfile &    
                             Append output to a file and run jt in the background