pregap, bourne vs C-shell

James Bonfield jkb at mrc-lmb.cam.ac.uk
Wed Mar 13 04:56:50 EST 1996

Stephen Baird wrote:

>Dear users of pregap,

>   Our normal shell on SUNOS 4.1.1 is the C-shell but pregap is a Bourne 
>shell script. For some unknown reason it does not always work. The main 
>problem seems to be during the use of "vepe" when rewriting the 
>${fofn}.passed file while using "sed" to remove the spaces from the 
>output files from vepe. It has worked sometimes but I can not figure out 

I can see no reason why this should go wrong. However there are numerous ways
of trimming white space from a file. I should probably have used "tr -d ' '"
instead, but tr tends to vary slightly between SysV and BSD systems. You could
try using awk or perl or something else too. The line in question though
should work fine on all systems so I really cannot find a problem. Any more
diagonostics would be useful. Try changing the first line to "#!/bin/sh -x" or
"#!/bin/sh -v" for debugging output.

>why. I'll rewrite the script as a C-Shell if no one knows what might 
>cause this problem. I keep thinking that the environment variables change 

Please don't! Csh is a terrible language. I wouldn't claim it to be the
"usual" shell either as all systems I know of have both sh and csh. If you
really want to know why I detest csh so much try working out how many 'A's
"repeat 3 repeat 3 echo A" would print. Or tell me why the following can't be
done on a single line "if ($?some_variable) echo $some_variable". I know csh
has some useful features, but as far as a language goes it's poor (in my

James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 412282
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/

More information about the Staden mailing list

Send comments to us at biosci-help [At] net.bio.net