BioNetFit.pbs

#!/bin/bash
#
# Version 1.1
# Written by Joshua Colvin
# jcolvin@tgen.org
#
# Function used to log every command that is executed.
# Takes two or three arguments:
#  - Directory command should be executed in.
#  - Command to execute.
#
#    Note that it is important to surround entire command with quotes
#    so that pipes and redirects are handled properly.
#
#  - If optional third argument is present, it contains the name of the file
#    to create if the program fails.
#    (make sure file doesn't exist before running)
#
# Example:
# echo_and_exec $PBS_O_WORKDIR "wc -l *.fastq > fastq_line_count.txt"
#
#
echo_and_exec()
{
  cd $1
  echo ""
  echo "In $1"
  echo "Running: $2"
  if [ ! "$test" ]
  then
   eval "$2"
  fi
  status=$?

  if [ ! $status == 0 ]
  then
    if [ "$3" ]
    then
      touch $3
    fi
    echo "Previous command returned error: $status"
    exit 1;
  fi
}

# Same but fork process so it runs in the background.
echo_and_exec_fork()
{
  cd $1
  
  cmd=${2//%%%/$1}
  
  echo ""
  echo "In $1"
  echo "Running: $cmd"
  eval "$cmd" &
  status=$?

  if [ ! $status == 0 ]
  then
    if [ "$3" ]
    then
      eval $3
    fi
    echo "Previous command returned error: $status"
    exit 1;
  fi
}

# List of variable names that are required to continue
# (names only, do not include '$')
#
# Example:
# require_var foo bar
#
require_var()
{
  for var in $*
  do
    eval if [ ! "\"\$$var\"" ]\; then echo "Oops, need variable $var\!"\; failed=1\; fi\;
  done

  if [ "$failed" ]
  then
    exit 1;
  fi

}

if [ ! $PBS_O_WORKDIR ]
then
  # Called from command line, not in PBS.
  PBS_O_WORKDIR="$PWD"
fi

if [ $SGE_O_WORKDIR ]
then
	PBS_O_WORKDIR="$SGE_O_WORKDIR"
fi

cd ${PBS_O_WORKDIR}

if [ -n "$command" ];
then
  echo_and_exec "$PBS_O_WORKDIR" "$command" "$touch_on_error"
fi

if [ -n "$command0" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command0" "$touch_on_error0"
fi

if [ -n "$command1" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command1" "$touch_on_error1"
fi

if [ -n "$command2" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command2" "$touch_on_error2"
fi

if [ -n "$command3" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command3" "$touch_on_error3"
fi

if [ -n "$command4" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command4" "$touch_on_error4"
fi

if [ -n "$command5" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command5" "$touch_on_error5"
fi

if [ -n "$command6" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command6" "$touch_on_error6"
fi

if [ -n "$command7" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command7" "$touch_on_error7"
fi

if [ -n "$command8" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command8" "$touch_on_error8"
fi

if [ -n "$command9" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command9" "$touch_on_error9"
fi

if [ -n "$command10" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command10" "$touch_on_error10"
fi

if [ -n "$command11" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command11" "$touch_on_error11"
fi

if [ -n "$command12" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command12" "$touch_on_error12"
fi

if [ -n "$command13" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command13" "$touch_on_error13"
fi

if [ -n "$command14" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command14" "$touch_on_error14"
fi

if [ -n "$command15" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command15" "$touch_on_error15"
fi

if [ -n "$command16" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command16" "$touch_on_error16"
fi

if [ -n "$command17" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command17" "$touch_on_error17"
fi

if [ -n "$command18" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command18" "$touch_on_error18"
fi

if [ -n "$command19" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command19" "$touch_on_error19"
fi

if [ -n "$command20" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command20" "$touch_on_error20"
fi

if [ -n "$command21" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command21" "$touch_on_error21"
fi

if [ -n "$command22" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command22" "$touch_on_error22"
fi

if [ -n "$command23" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command23" "$touch_on_error23"
fi

if [ -n "$command24" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command24" "$touch_on_error24"
fi

if [ -n "$command25" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command25" "$touch_on_error25"
fi

if [ -n "$command26" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command26" "$touch_on_error26"
fi

if [ -n "$command27" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command27" "$touch_on_error27"
fi

if [ -n "$command28" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command28" "$touch_on_error28"
fi

if [ -n "$command29" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command29" "$touch_on_error29"
fi

if [ -n "$command30" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command30" "$touch_on_error30"
fi

if [ -n "$command31" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command31" "$touch_on_error31"
fi

if [ -n "$command32" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command32" "$touch_on_error32"
fi

if [ -n "$command33" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command33" "$touch_on_error33"
fi

if [ -n "$command34" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command34" "$touch_on_error34"
fi

if [ -n "$command35" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command35" "$touch_on_error35"
fi

if [ -n "$command36" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command36" "$touch_on_error36"
fi

if [ -n "$command37" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command37" "$touch_on_error37"
fi

if [ -n "$command38" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command38" "$touch_on_error38"
fi

if [ -n "$command39" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command39" "$touch_on_error39"
fi

if [ -n "$command40" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command40" "$touch_on_error40"
fi

if [ -n "$command41" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command41" "$touch_on_error41"
fi

if [ -n "$command42" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command42" "$touch_on_error42"
fi

if [ -n "$command43" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command43" "$touch_on_error43"
fi

if [ -n "$command44" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command44" "$touch_on_error44"
fi

if [ -n "$command45" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command45" "$touch_on_error45"
fi

if [ -n "$command46" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command46" "$touch_on_error46"
fi

if [ -n "$command47" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command47" "$touch_on_error47"
fi

if [ -n "$command48" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command48" "$touch_on_error48"
fi

if [ -n "$command49" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command49" "$touch_on_error49"
fi

if [ -n "$command50" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command50" "$touch_on_error50"
fi

if [ -n "$command51" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command51" "$touch_on_error51"
fi

if [ -n "$command52" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command52" "$touch_on_error52"
fi

if [ -n "$command53" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command53" "$touch_on_error53"
fi

if [ -n "$command54" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command54" "$touch_on_error54"
fi

if [ -n "$command55" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command55" "$touch_on_error55"
fi

if [ -n "$command56" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command56" "$touch_on_error56"
fi

if [ -n "$command57" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command57" "$touch_on_error57"
fi

if [ -n "$command58" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command58" "$touch_on_error58"
fi

if [ -n "$command59" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command59" "$touch_on_error59"
fi

if [ -n "$command60" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command60" "$touch_on_error60"
fi

if [ -n "$command61" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command61" "$touch_on_error61"
fi

if [ -n "$command62" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command62" "$touch_on_error62"
fi

if [ -n "$command63" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command63" "$touch_on_error63"
fi

if [ -n "$command64" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command64" "$touch_on_error64"
fi

if [ -n "$command65" ];
then
  echo_and_exec_fork "$PBS_O_WORKDIR" "$command65" "$touch_on_error65"
fi

wait