C Shell Scripting

Header information

#!/bin/tcsh                 indicates that the script is writing in tcsh
#PBS -l nodes=1:ppn=2       use 1 node and 2 processors per node
#PBS -l walltime=01:00:00   run for a maximum time of 1 hour
#PBS -N dock6               set the name of the job to 'dock6'
#PBS -M user@sunysb.edu     your e-mail address (optional)
#PBS -j oe                  join the output and error files
#PBS -o pbs.out             set the output name to 'pbs.out'

General commands

set var = 'value'           assign 'value' to the variable 'var'
@var = $var + 1             modify the assignment of 'var' (increment by 1)
echo $var                   print the contents of the variable 'var'

If / else

set number = 5
if (number < 9) then
   echo 'less than 9'
else
   echo 'Greater than 9'
endif

Expected output:
         less than 9

Foreach loop

foreach var (1AIK 2PK8 3O3X)
   mkdir $var
   echo 'Just made the new dir' $var
end

Expected output:
         Just made the new dir 1AIK
         Just made the new dir 2PK8
         Just made the new dir 3O3X

While loop

set count = 1
echo $count
while ($count <= 10)
  echo Count = $count
  @ count ++
end

Expected output:
       1
       Count = 1
       Count = 2
       Count = 3
       ...
       Count = 10

Other things to know

#  Any text that comes after a '#' sign is ignored, other than the special cases shown above. This is a useful way to make comments in the scripts.