bashgnu-parallelmultiple-arguments

How to run on BASH a python script that takes multiple arguments using GNU parallel?

I have a python script which I normally execute from BASH shell like this:

pychimera $(which dockprep.py) -rec receptor1.pdb -lig ligand1.mol -cmethod gas -neut

As you see some of the arguments need an input (e.g. -rec) while others don't (e.g. -neut). I must execute this script 154 times with different inputs. How is it possible to run 8 threads in parallel using GNU parallel script?

pychimera $(which dockprep.py) -rec receptor1.pdb -lig ligand1.mol -cmethod gas -neut
pychimera $(which dockprep.py) -rec receptor2.pdb -lig ligand2.mol -cmethod gas -neut
pychimera $(which dockprep.py) -rec receptor3.pdb -lig ligand3.mol -cmethod gas -neut
...
Solution

  • Example commands.txt generator script:

    #!/usr/bin/env bash

if [ "$#" -ne 1 ]; then
    echo "missing parameter: n"
    exit 1
fi

rm commands.txt 2> /dev/null 
dockp=$(which dockprep.py)

for((i=1;i<=$1;i++)); do
  echo "pychimera $dockp -rec receptor$i.pdb -lig ligand$i.mol -cmethod gas -neut" >> commands.txt
done

    If you save above bash script as cmdgen.sh you can run it as:

    bash cmdgen.sh 100

    if you need n to be 100.

    To run commands in parallel:

    $ module load parallel
$ parallel < commands.txt