C Shell Scripts

These scripts must be executable.

$ chmod 775 myscript.com

Sample 1

This file aim2voi.com shows the use of command line arguments in a CSH script.

#!/bin/csh
#------------------------------------------------------------------------------
onintr end
if ($#argv < 1) goto usage
#------------------------------------------------------------------------------
aix $1.aim > $1.dsc
aic2voi $1.aim $1.voi
goto end
#------------------------------------------------------------------------------
usage:
#
echo ""
echo "Usage:"
echo ""
echo "aim2voi aim_filename (without aim extension)"
echo "will create a voi and dsc file from an aim"
echo ""
#
exit
#------------------------------------------------------------------------------
end:
exit
#------------------------------------------------------------------------------

Sample 2

Similar to above, but aim2bid.com generates a temporary file called stack which is used as input.

#!/bin/csh
#------------------------------------------------------------------------------
onintr end
if ($#argv < 4) goto usage
#------------------------------------------------------------------------------
set i = $3
while ($i <= $4)
  set nr = $i
  if ($nr<10)  set nr = "0"$nr""
  if ($nr<100) set nr = "0"$nr""
#  if ($nr<1000) set nr = "0"$nr""
  echo "XY" >! stack
  echo "$i" >> stack
  echo "$5" >> stack
  if ($6 != "") then
    echo "0" >> stack
    aio $1 "$2"_"$nr".bid 14 < stack
    convert -size "$7" "$2"_"$nr".bid "$2"_"$nr"."$6"
    \rm -f "$2"_"$nr".bid
  else
    echo "2" >> stack
    aio $1 "$2"_"$nr".bid 14 < stack
  endif
  \rm -f stack
  @ i = $i + 1
end
goto end
#------------------------------------------------------------------------------
usage:
#
echo ""
echo "Usage:"
echo ""
echo "aim2bid aim_filename bid_prefix first_slice last_slice scal_factor [form size])"
echo "                                (values are one-based)              gif/tif/..."
echo ""
#
exit
#------------------------------------------------------------------------------
end:
exit
#------------------------------------------------------------------------------

Sample 3

An example where a sequence of commands are executed resulting in an e-mail to let the user know that their job is finished.

#!/bin/csh
# 
nohup faim -s $1; /bin/csh -cbf "Mail -s 'JOB $1 FINISHED' boyd@kin < ~/adm/mailer/faimjob.txt" &

You would run this script called faim.com as follows

$ faim.com inputfile

Sample 4

This example uses two files. One called wrap.com is the base program that is called in a more general program called wrap_all.com so that many different files can be processed by the base script.

• wrap.com

#!/bin/csh

echo "0" >! stack
echo "0" >> stack
echo "0" >> stack

/home/skb/works/fio/aim_io $1.aim $1_sub.aim minimal 15 < stack

/rm -f stack

exit

• wrap_all.com

#!/bin/csh

~/works/com/wrap calgary_dog_aclx_03-04_med_fem_left
~/works/com/wrap calgary_dog_aclx_03-04_med_fem_right
~/works/com/wrap calgary_dog_aclx_03-04_med_tib_left
~/works/com/wrap calgary_dog_aclx_03-04_med_tib_right

echo "DONE!"
exit