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.
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
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.
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!
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 backgroundUpdated 07/12/2001