qsub1line

#!/usr/bin/perl
use warnings;
use strict;
use FindBin;
my $bindir = $FindBin::Bin;

##############################################################################
#   Copyright notice:   Copyright (c) Richard Yim, 16 Aug 2016, v1.1
#                       All rights reserved.
#
#   Contributors: Richard Yim*
#
#  *Department of Cancer Biology
#   Cancer Institute
#   University College London
#
#   THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 
#   "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED 
#   TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR 
#   PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR 
#   CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 
#   EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, 
#   PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
#   PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 
#   LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 
#   NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
#   SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
#   You are free to use, distribute and/or modify this software as you wish as
#   long as the following conditions are met:
#   The software must retain this copyright notice.
#   Contributors must add their names to the contributors list.
#   Neither the name of the copyright holder nor the names of its contributors 
#   may be used to endorse or promote products derived from this software
#   without specific prior written permission.
#
##############################################################################
#
#   INSTALLATION
#   Place the files qsub1line and qsub1line in a directory in a writeable
#   filesystem.
#   Add this directory to your $PATH in your chosen environment config file
#   (E.G.: ~/.bashrc).
#
##############################################################################

#   Check all files are present
my @dependencies = (
    $bindir . "/qsub1line.template"
);
my $missingdependencies = 0;
foreach my $file (@dependencies) {
    unless (-e $file) {
        print "Fatal error: Missing dependency:\n$file\n";
        $missingdependencies = 1;
    }
}
exit(1) if $missingdependencies == 1;       # Crap out if missing files

#   General idiotproofing
if (!$ARGV[0]) {
    print "Invalid input. Usage: \"qsub1line <command> [arguments]\"\n";
    exit(1);
} elsif ($ARGV[1]) {
    print "Put command and its arguments in double quotes: \"\"\n";
    exit(1);
}

#   Parse in command line
my $command = $ARGV[0];
(my $procname = $command) =~ s/\s.*//;      # Set a name for process
print "Process name:\t$procname\nCommand passed:\t$command\n";

#   Write qsub script so Legion people are happy
open(IN, $bindir . "/qsub1line.template");
open(OUT, ">$bindir/.qsub1line.temp")
    or die "Script not in writeable filesystem.\n";
foreach my $line (<IN>) {
    $line =~ s/NAME/$procname/g;
    $line =~ s/COMMAND/$command/g;
    print OUT $line;
}
close(OUT);
close(IN);

#   Run qsub script
system("qsub $bindir/.qsub1line.temp");