Revision as of 10:29, 26 March 2010 by Teuben (Talk | contribs)

Jump to: navigation, search

drPACS is a simple yet flexible and effective pipeliner for Unix commands. There is a document (currently Appendix A in the PACS cookbook) describing this is more detail,but here is just a teaser to get a feel for what you can do with it.

Assuming it has been installed, a $DRPACS environment variable points to where the code lives, and normally $DRPACS/bin will have been added to your search path.


Simple examples how to start

Step 1: generate the control Pipefile (hint: it's a Makefile)

  pipeline $DRPACS/cat/pipeline.001 > Pipefile
  pipeline 4 step1 step2 step3 step4 > Pipefile

Step 2: set some parameters

  pipepar -c
  pipepar -c project=c0184.3B_108PG2130.13 carmaRefant=2
  pipepar interval=5 carmaRefant=3

Step 3: run the pipe

  pipe all
  pipe step2
  pipe all
  pipe clean

more advanced examples

Running pipeline in a set of directories

method 1: old-style c-shell method

  foreach dir (`cat dirs.txt`)
    cd $dir
    pipepar foo=3.3
    pipe step3 all
    cd ..

method 2: using piperun

  piperun dirs.txt 'pipepar foo=3.3 ;  pipe step3 all'

Scatterplot from a set of directories

  piperun dirs.txt pipepar -v foo -v bar > foo_bar.tab
  tabplot foo_bar.tab

Parallel pipe

  piperun -n 4 dirs.txt pipe step2 all

PACS, in parallel

  piperun -n 4 -c -o pipe.log dirs.txt 'pipepar -c project=%s showPlots=False; pipe clean all'

pipe scripts in csh

#! /bin/csh -f
#   (1) define default values in case not given
set a=1
set b=2
#  (2) pipeline interface to grab old defaults
pipepar -s csh > tmp$$.par;  source tmp$$.par;  rm tmp$$.par
#  (3) poor man's command line processor to override parameters
foreach _arg ($*)
 set $_arg
#  (4) The Actual Code where the work can be done
echo A=$a   B=$b
#  (5) write pipeline parameters back
pipepar a=$a b=$b c=3

pipe scripts in python

#! /bin/env python
import parfile, sys
if __name__ == "__main__":
  p = parfile.Parfile('drpacs.def')
  if p.has('b'): 
     b = p.get('b')
Personal tools