runNuclDyn

#!/usr/bin/perl
#  Copyright 2019 Barcelona Supercomputing Center
#  
#  Licensed under the Apache License, Version 2.0 (the "License");
#  you may not use this file except in compliance with the License.
#  You may obtain a copy of the License at
#  
#      http://www.apache.org/licenses/LICENSE-2.0
#  
#  Unless required by applicable law or agreed to in writing, software
#  distributed under the License is distributed on an "AS IS" BASIS,
#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#  See the License for the specific language governing permissions and
#  limitations under the License.

  
#
# runNuclDyn: launcher for Nucl. Dynamics executables
# Authors: Josep Ll. Gelpi 2018
# Authors: Marc del Pino 2019
use strict;
use File::Basename;
use Cwd;

my $RSCRIPT = "/usr/bin/Rscript";
my $NDDIR = "/home/NucleosomeDynamics";

if (! -d $NDDIR){
	my $lo = dirname($0);
	$lo =~ s/\.//g;
	$NDDIR = cwd().$lo;
}

my $BINDIR = "$NDDIR/NucleosomeDynamics/bin";
my $STATSDIR = "$NDDIR/NucleosomeDynamics/statistics";
my $HELPDIR = "$NDDIR/help";

# my $DATADIR = "/data_dir";     # used to find DATADIR/scripts/user_wf.file
# my $PUBLICDIR = "/public_dir"; # OBSOLETE

my $FUNCTIONS = ['run','readBAM','nucleR','NFR','txstart','periodicity','stiffness','nucDyn','nucleR2structure','toBigWig','fromBigWig','coverage','js_plot'];
my $FUNCTIONS_STATS = ['nucleR_stats','NFR_stats','txstart_stats','periodicity_stats','stiffness_stats','nucDyn_stats'];

#
system ("/bin/cat $HELPDIR/header.txt");

# Main Help

if (!@ARGV || ($ARGV[0] eq '--help') || ($ARGV[0] eq '-h')) {
    system ("/bin/cat $HELPDIR/main.hlp");
    exit;
}

my $op = shift;

if (!is_valid_function($op) && !is_valid_function_stats($op)) {
    die "\nError: unrecognized function $op, try [-h |--help]\n\n";
}

#Specific help
if (!@ARGV || ($ARGV[0] eq '--help') || ($ARGV[0] eq '-h')) {
    system ("/bin/cat $HELPDIR/$op.hlp");
    exit;
}

# Running tool
#
my $hasError_file = "/tmp/hasError".rand();
my $cmd_catchErr = "while read line; do echo \$line; if echo \${line} | grep -iqP 'ERROR'; then echo \${line}  >  $hasError_file;  fi;  done";

#if (-e $DATADIR) {
     #chdir $DATADIR;
# }

if ($op eq "run") {
    print "===> Running $op <===\n\n";
    system ("/bin/sh @ARGV 2>&1 | $cmd_catchErr");
} else {
    print "===> Running $op <===\n\n";
    if (($op =~ /stats/) && is_valid_function_stats($op)) {
	$op =~ s/_stats//g;
        my $args_str = join(" ",@ARGV);
        my $cmd = "$RSCRIPT $STATSDIR/$op.R $args_str 2>&1 | $cmd_catchErr\n";
	system($cmd);
    } elsif (is_valid_function($op)) {
        my $args_str = join(" ",@ARGV);
        my $cmd = "$RSCRIPT $BINDIR/$op.R $args_str 2>&1 | $cmd_catchErr\n";
        system ($cmd);
    } else {
        system ("/bin/cat $HELPDIR/main.hlp");
    }
}

# Catch error
#
if (-e  $hasError_file){
	print STDERR "ERROR while running $op. Check the full report at 'stdout'\n";
}

sub is_valid_function {
   my $f = shift;
   return _is_valid($f, $FUNCTIONS);
}

sub is_valid_function_stats {
   my $f = shift;
   return _is_valid($f, $FUNCTIONS_STATS);
}

sub _is_valid {
  my ($f, $list) = @_;
  my $i=0;
  
  while (($i<$#{$list}) && ($list->[$i] ne $f)) {$i++};
  return ($list->[$i] eq $f);
}