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#!/usr/bin/perl -w
#
# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
#
# This file is part of Bowtie 2.
#
# Bowtie 2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Bowtie 2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
#
use strict;
use warnings;
use Getopt::Long;
use FindBin qw($Bin);
use lib "$Bin";
use lib "$Bin/contrib";
use Sim;
use ForkManager;
# Simulator configuration
our %conf = (
bowtie2_build => "bowtie2-build",
bowtie2 => "bowtie2",
bowtie2_build_debug => "bowtie2-build --debug",
bowtie2_debug => "bowtie2 --debug",
tempdir => "/tmp",
no_color => 1,
small => 1
);
# Number of parallel processes to use
my $cpus = 1;
my $usage = qq!
run.pl [options*]
Options:
--bowtie2 <path> Path to bowtie2 release binary
--bowtie2-debug <path> Path to bowtie2 debug binary
--bowtie2-build <path> Path to bowtie2-build release binary
--bowtie2-build-debug <path> Path to bowtie2-build debug binary
--tempdir <path> Put temporary files here
--cases <int> Each thread runs around <int> cases (def: 5)
--cpus <int> / -p <int> Run test cases in <int> threads at once
--maxreads <int> Handle at most <int> reads per case
--numrefs <int> Generate <int> refs per case
--die-with-child Kill parent as soon as 1 child dies
--no-die-with-child Don\'t kill parent as soon as 1 child dies
--small Make small test cases
--help Print this usage message
!;
my $help = 0;
my $ncases = 5;
my $dieWithChild = 1;
GetOptions(
"bowtie2=s" => \$conf{bowtie2},
"bowtie2-build=s" => \$conf{bowtie2_build},
"tempdir|tmpdir=s" => \$conf{tempdir},
"cases-per-thread=i" => \$ncases,
"small" => \$conf{small},
"large" => sub { $conf{small} = 0 },
"no-paired" => \$conf{no_paired},
"color" => sub { $conf{no_color} = 0 },
"no-color" => \$conf{no_color},
"help" => \$help,
"die-with-child" => \$dieWithChild,
"no-die-with-child" => sub { $dieWithChild = 0 },
"p|cpus=i" => \$cpus,
"u|qupto|maxreads=i" => \$conf{maxreads},
"numrefs|num-refs=i" => \$conf{numrefs},
) || die "Bad options;";
if($help) {
print $usage;
exit 0;
}
my $sim = Sim->new();
my $pm = new Parallel::ForkManager($cpus);
# Callback for when a child finishes so we can get its exit code
my @childFailed = ();
my @childFailedPid = ();
$pm->run_on_finish(sub {
my ($pid, $exit_code, $ident) = @_;
if($exit_code != 0) {
push @childFailed, $exit_code;
push @childFailedPid, $pid;
!$dieWithChild || die "Dying with child with PID $pid";
}
});
my $totcases = $ncases * $cpus;
for(1..$totcases) {
my $childPid = $pm->start;
if($childPid != 0) {
next; # spawn the next child
}
$sim->nextCase(\%conf);
$pm->finish;
}
$pm->wait_all_children;
for(@childFailedPid) {
print STDERR "Error message from child with pid $_:\n";
my $fn = ".run.pl.child.$_";
if(open(ER, $fn)) {
print STDERR "---------\n";
while(<ER>) {
print STDERR $_;
}
print STDERR "---------\n";
close(ER);
} else {
print STDERR "(could not open $fn)\n";
}
}
print STDERR "PASSED\n";
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