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#!/usr/bin/env perl
use strict;
use warnings;
use Cwd;
use File::Basename;
my $usage = "usage: $0 cNumb.graph\n\n";
my $comp = $ARGV[0] or die $usage;
my $TRINITY_HOME = $ENV{TRINITY_HOME} or die "Error, need env var TRINITY_HOME";
main: {
my $base_comp_name = basename($comp);
my $cwd = cwd();
unless ($comp =~ /^\//) {
$comp = "$cwd/$comp";
}
{ ## run old butterfly
my $workdir = "$cwd/__$base_comp_name.oldBfly_dir";
mkdir($workdir) or die "Error, cannot mkdir $workdir";
chdir $workdir or die $!;
my $cmd = "ln -s $comp.reads .; ln -s $comp.out .";
&process_cmd($cmd);
$cmd = "java -Xmx4G -jar $/usr/share/java/Butterfly.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 --max_number_of_paths_per_node=10 -V 15 --stderr 2>&1 | tee log.txt";
open (my $ofh, ">bfly.cmd") or die $!;
print $ofh $cmd;
close $ofh;
&process_cmd($cmd);
}
chdir $cwd or die $!;
{ ## run new butterfly
my $workdir = "$cwd/__$base_comp_name.newBfly_dir";
mkdir($workdir) or die $!;
chdir ($workdir) or die $!;
my $cmd = "ln -s $comp.reads .; ln -s $comp.out .";
&process_cmd($cmd);
$cmd = "java -Xmx4G -jar /usr/share/java/Butterfly.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 -V 15 --stderr 2>&1 | tee log.txt";
open (my $ofh, ">bfly.cmd") or die $!;
print $ofh $cmd;
close $ofh;
&process_cmd($cmd);
}
exit(0);
}
####
sub process_cmd {
my ($cmd) = @_;
print STDERR "CMD: $cmd\n";
my $ret = system($cmd);
if ($ret) {
die "Error, CMD: $cmd died with ret $ret";
}
return;
}
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