96 lines
1.9 KiB
Perl
96 lines
1.9 KiB
Perl
#!/usr/bin/env perl
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use strict;
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use warnings;
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use Cwd;
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use File::Basename;
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my $usage = "usage: $0 cNumb.graph\n\n";
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my $comp = $ARGV[0] or die $usage;
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my $TRINITY_HOME = $ENV{TRINITY_HOME} or die "Error, need env var TRINITY_HOME";
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main: {
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my $base_comp_name = basename($comp);
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my $cwd = cwd();
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unless ($comp =~ /^\//) {
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$comp = "$cwd/$comp";
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}
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{ ## run old butterfly
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my $workdir = "$cwd/__$base_comp_name.oldBfly_dir";
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mkdir($workdir) or die "Error, cannot mkdir $workdir";
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chdir $workdir or die $!;
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my $cmd = "ln -s $comp.reads .; ln -s $comp.out .";
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&process_cmd($cmd);
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$cmd = "java -Xmx4G -jar $TRINITY_HOME/Butterfly/prev_vers/Butterfly_r2013_08_14.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 --max_number_of_paths_per_node=10 -V 15 --stderr 2>&1 | tee log.txt";
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open (my $ofh, ">bfly.cmd") or die $!;
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print $ofh $cmd;
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close $ofh;
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&process_cmd($cmd);
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}
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chdir $cwd or die $!;
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{ ## run new butterfly
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my $workdir = "$cwd/__$base_comp_name.newBfly_dir";
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mkdir($workdir) or die $!;
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chdir ($workdir) or die $!;
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my $cmd = "ln -s $comp.reads .; ln -s $comp.out .";
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&process_cmd($cmd);
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$cmd = "java -Xmx4G -jar $TRINITY_HOME/Butterfly/Butterfly.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 -V 15 --stderr 2>&1 | tee log.txt";
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open (my $ofh, ">bfly.cmd") or die $!;
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print $ofh $cmd;
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close $ofh;
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&process_cmd($cmd);
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}
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exit(0);
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}
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####
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sub process_cmd {
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my ($cmd) = @_;
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print STDERR "CMD: $cmd\n";
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my $ret = system($cmd);
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if ($ret) {
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die "Error, CMD: $cmd died with ret $ret";
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}
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return;
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}
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