#!/usr/bin/env perl

# DO NOT EDIT the /cluster/bin/scripts copy of this file --
# edit ~/kent/src/hg/utils/automation/doTemplate.pl instead.

# $Id: doTemplate.pl,v 1.2 2007/08/13 20:45:19 angie Exp $

# HOW TO USE THIS TEMPLATE:
# 1. Global-replace doTemplate.pl with your actual script name.
# 2. Search for template and replace each instance with something appropriate.
#    Add steps and subroutines as needed.  Other do*.pl or make*.pl may have
#    useful example code -- this is just a skeleton.

use Getopt::Long;
use warnings;
use strict;
use FindBin qw($Bin);
use lib "$Bin";
use HgAutomate;
use HgRemoteScript;
use HgStepManager;

# Option variable names, both common and peculiar to this script:
use vars @HgAutomate::commonOptionVars;
use vars @HgStepManager::optionVars;
use vars qw/
    $opt_buildDir
    /;

# Specify the steps supported with -continue / -stop:
my $stepper = new HgStepManager(
    [ { name => 'template',   func => \&doTemplate },
      { name => 'cleanup', func => \&doCleanup },
    ]
				);

# Option defaults:
my $dbHost = 'hgwdev';

my $base = $0;
$base =~ s/^(.*\/)?//;

sub usage {
  # Usage / help / self-documentation:
  my ($status, $detailed) = @_;
  # Basic help (for incorrect usage):
  print STDERR "
usage: $base db
options:
";
  print STDERR $stepper->getOptionHelp();
  print STDERR <<_EOF_
    -buildDir dir         Use dir instead of default
                          $HgAutomate::clusterData/\$db/$HgAutomate::trackBuild/template.\$date
                          (necessary when continuing at a later date).
_EOF_
  ;
  print STDERR &HgAutomate::getCommonOptionHelp('dbHost' => $dbHost,
						'workhorse' => '',
						'fileServer' => '',
						'bigClusterHub' => '',
						'smallClusterHub' => '');
  print STDERR "
Automates UCSC's template.  db is just a template arg.  Steps:
    template: template
    cleanup: Removes or compresses intermediate files.
All operations are performed in the build directory which is
$HgAutomate::clusterData/\$db/$HgAutomate::trackBuild/template.\$date unless -buildDir is given.
";
  # Detailed help (-help):
  print STDERR "
Assumptions:
1. $HgAutomate::clusterData/\$db/\$db.2bit contains RepeatMasked sequence for
   database/assembly \$db.
2. $HgAutomate::clusterData/\$db/chrom.sizes contains all sequence names and sizes from
   \$db.2bit.
3. The \$db.2bit files have already been distributed to cluster-scratch
   (/scratch/hg or /iscratch, /san etc).
4. template?
" if ($detailed);
  print "\n";
  exit $status;
}


# Globals:
# Command line args: db
my ($db);
# Other:
my ($buildDir, $secondsStart, $secondsEnd);

sub checkOptions {
  # Make sure command line options are valid/supported.
  my $ok = GetOptions(@HgStepManager::optionSpec,
		      'buildDir=s',
		      @HgAutomate::commonOptionSpec,
		      );
  &usage(1) if (!$ok);
  &usage(0, 1) if ($opt_help);
  &HgAutomate::processCommonOptions();
  my $err = $stepper->processOptions();
  usage(1) if ($err);
  $dbHost = $opt_dbHost if ($opt_dbHost);
}


#########################################################################
# * step: template [workhorse]
sub doTemplate {
  my $runDir = "$buildDir/run.template";
  &HgAutomate::mustMkdir($runDir);

  my $whatItDoes = "It templates.";
  my $workhorse = &HgAutomate::chooseWorkhorse();
  my $bossScript = new HgRemoteScript("$runDir/doTemplate.csh", $workhorse,
				      $runDir, $whatItDoes);

  $bossScript->add(<<_EOF_
template csh commands
_EOF_
  );
  $bossScript->execute();
} # doTemplate


#########################################################################
# * step: cleanup [fileServer]
sub doCleanup {
  my $runDir = "$buildDir";
  my $whatItDoes = "It cleans up or compresses intermediate files.";
  my $fileServer = &HgAutomate::chooseFileServer($runDir);
  my $bossScript = new HgRemoteScript("$runDir/doCleanup.csh", $fileServer,
				      $runDir, $whatItDoes);
  $bossScript->add(<<_EOF_
rm -rf run.template/raw/
rm -rf templateOtherBigTempFilesOrDirectories
gzip template
_EOF_
  );
  $bossScript->execute();
} # doCleanup


#########################################################################
# main

# Prevent "Suspended (tty input)" hanging:
&HgAutomate::closeStdin();

# Make sure we have valid options and exactly 1 argument:
&checkOptions();
&usage(1) if (scalar(@ARGV) != 1);
$secondsStart = `date "+%s"`;
chomp $secondsStart;
($db) = @ARGV;

# Force debug and verbose until this is looking pretty solid:
$opt_debug = 1;
$opt_verbose = 3 if ($opt_verbose < 3);

# Establish what directory we will work in.
my $date = `date +%Y-%m-%d`;
chomp $date;
$buildDir = $opt_buildDir ? $opt_buildDir :
  "$HgAutomate::clusterData/$db/$HgAutomate::trackBuild/template.$date";

# Do everything.
$stepper->execute();

# Tell the user anything they should know.
my $stopStep = $stepper->getStopStep();
my $upThrough = ($stopStep eq 'cleanup') ? "" :
  "  (through the '$stopStep' step)";

$secondsEnd = `date "+%s"`;
chomp $secondsEnd;
my $elapsedSeconds = $secondsEnd - $secondsStart;
my $elapsedMinutes = int($elapsedSeconds/60);
$elapsedSeconds -= $elapsedMinutes * 60;

&HgAutomate::verbose(1,
	"\n *** All done !$upThrough  Elapsed time: ${elapsedMinutes}m${elapsedSeconds}s\n");
&HgAutomate::verbose(1,
	" *** Steps were performed in $buildDir\n");
&HgAutomate::verbose(1, "\n");