#!/usr/bin/perl
use strict;

use lib "$ENV{GUS_HOME}/lib/perl";
use GUS::Pipeline::Manager;
use GUS::Pipeline::MakeTaskDirs;
use GUS::Pipeline::NfsCluster;
use GUS::Pipeline::SshCluster;
use CBIL::Util::PropertySet;
use CBIL::Util::GenomeDir;
use File::Basename;

# the "Steps" module contains all the pipeline-step routines
# that are called below.

use ApiComplexa::DataLoad::Steps;

$| = 1;
umask 002;


my $propertiesFile = $ARGV[0];

&usage unless -e $propertiesFile;

# [name, default (or null if reqd), comment]
my @properties = 
(
 # properties required by Pipeline API  - incomplete, waiting for steps
 ["blastmatrix.taskSize", "",  "number of seqs to process per blastmatrix subtask"],
 ["blastsimilarity.params", "", "paramters for blastsimilarity"],
 ["blastsimilarity.taskSize", "",  "number of seqs to process per blastsimilarity subtask"],
 ["buildDir",   "",  "root of the build's directory tree"],
 ["cap4Dir", "", "directory containing executable cap4"],
 ["clusterServer", "",  "full name of cluster server"],
 ["contigDbName", "", "sres.externaldatabase.name for contigs"],
 ["contigDbRlsVer", "", "sres.externaldatabaserelease.version for contigs"]
 ["externalDbDir", "", "directory for downloading data from external databases"],
 ["fileOfRepeats", "", "repeat file for use by repeatmasker"],
 ["gb_db_rel_id", "", "genbank external_database_release_id"],
 ["genusNickname", "", "e.g Crypto"],
 ["gusConfigFile",           "",  ""],
 ["includeSubspecies", "", "yes or no, get a list of taxon_ids for the subspecies of the given taxon_id(ncbi_tax_id)"],
 ["intermedCluster.length",  "",  "min length cut-off for clustering algorithm"],
 ["intermedCluster.percent",  "",  "min percent identity cutoff for clustering algorithm"],
 ["intermedCluster.logbase",  "",  ""],
 ["intermedCluster.consistentEnds",  "",  "requirement for consistent ends, yes or no"],
 ["intermedCluster.cliqueSzArray",  "",  ""],
 ["intermedCluster.logbaseArray",  "",  ""],
 ["gusConfigFile",  "",  "gus configuration file"],
 ["loadcontigs-nrdbRestart",  "",  "algorithm_invocation_id(s) of previous starts, for restart of BLAST similarity loading plugin"],
 ["nrdbDbName" , "","the externaldatabase.name for nrdb"],
 ["nrdbDbRlsVer" , "","the externaldatabaserelease.version for the current nrdb"],
 ["nodePath",             "",  "full path of scratch dir on cluster node"],
 ["phrapDir",             "",  "full path of directory containing phrap software"],
 ["projectId",             "",  "project_id from core.projectInfo"],
 ["release",   "",  "build release number"],
 ["repeatmask.dangleMax", "","option for trimDangling in repeatMasker"],
 ["repeatmask.options",   "",  "number of seqs to process per blastmatrix subtask"],
 ["repeatmask.path",      "",  "path on node of repeatmask executable"],
 ["repeatmask.taskSize",  "",  "number of seqs to process per repeatmask subtask"],
 ["serverPath", "",  "full path of update dir on cluster server"],
 ["speciesNickname", "",  "eg cparvum"],
 ["speciesFullname", "", "eg Cryptosporidium parvum"],
 ["stopBefore",   "none",  "the step to stop before.  uses the signal name"],
 ["taskSize",  "",  "number of seqs to process per subtask"],
 ["ncbiTaxId", "", "tax_id from NCBI taxonomy db"],
 ["testNextPlugin", "false", "'true' to run in no-commit mode the first plugin not yet done and then exit"],
 ["wuBlastBinPathCluster",         "",  "path of wu blast bin dir on Liniac"],
 ); 

my $propertySet  = CBIL::Util::PropertySet->new($propertiesFile, \@properties, 1);

my $buildDir = $propertySet->getProp('buildDir');
my $release = $propertySet->getProp('release');
my $genusNickname = $propertySet->getProp('genusNickname');
my $buildName = "$release/analysis_pipeline/$genusNickname";
my $pipelineDir = "$buildDir/$buildName";

##########################  The Pipeline  ##########################

my $cluster;
if ($propertySet->getProp('clusterServer') ne "none") {
  $cluster = GUS::Pipeline::SshCluster->new($propertySet->getProp('clusterServer'),
					  $propertySet->getProp('clusterUser') );
} else {
  $cluster = GUS::Pipeline::NfsCluster->new();
}

my $mgr = GUS::Pipeline::Manager->new($pipelineDir, $propertySet, 
				      $propertiesFile, $cluster, 
				      $propertySet->getProp('testNextPlugin'));


$mgr->{buildName} = $buildName;
$mgr->{pipelineDir} = $pipelineDir;
$mgr->{propertiesFile} = $propertiesFile;
$mgr->{propertySet} = $propertySet;

my $taxonId = &getTaxonIdFromTaxId($mgr);
$mgr->{taxonId} = $taxonId;

&createPipelineDir($mgr); 

&createBlastMatrixDir($mgr,"intermedTranscriptCons", "intermedTranscriptCons");

&createBlastMatrixDir($mgr,"intermedTranscriptCons", "unallignededTranscripts");

&createBlastMatrixDir($mgr,"unallignededTranscripts", "unallignededTranscripts");

&createSimilarityDir($mgr,"contigs","nrdb","(\d+)","matrix=BLOSUM62 V=100 B=1000000 -hspmax=1000000 W=4 T=18 -gi E=1e-3 - wordmask=seg -hspsepQmax=50000","blastx");

&createSimilarityDir($mgr,"annotatedproteins","nrdb","(\d+)","matrix=BLOSUM62  -topcomboN=1 V=10 B=10 W=4 T=18 -span1 -gi E=1e-3 -wordmask=seg","blastp");

&createRepeatMaskDir($mgr,"newTranscripts");

&createRepeatMaskDir($mgr,"intermedTranscriptCons");

&createRepeatMaskDir($mgr,"unalignedTranscripts");

&createRepeatMaskDir($mgr,"finalTranscriptCons");

&createGenomeDir($mgr,"newTranscripts", "contigs");   

&createGenomeDir($mgr,"finalTranscriptCons", "contigs");

&copyPipelineDirToComputeCluster($mgr);

&extractContigs($mgr);    

&copyFilesToComputeCluster($mgr,"contigs"); # signal contigsExtract

&extractNRDB($mgr);   

&copyFilesToComputeCluster($mgr,"nrdb");  

&startProteinBlastOnComputeCluster($mgr,"nrdb");  

&copyFilesFromComputeCluster($mgr,"contigs-nrdb","similarity"); 

&loadProteinBlast($mgr, "contigs-nrdb","DoTS::ExternalAASequence"); 

&extractAnnotatedProteins($mgr);

&copyFilesToComputeCluster($mgr,"annotatedProteins");

&startProteinBlastOnComputeCluster($mgr,"annotatedProteins");

&copyFilesFromComputeCluster($mgr,"annotatedProteins-nrdb","similarity");

&loadProteinBlast($mgr, "annotatedproteins-nrdb","DoTS::TranslatedAASequence");

&makeTranscriptSeqs($mgr);

&extractTranscriptSeqs($mgr,"newTranscripts");

&copyFilesToComputeCluster($mgr,"newTranscripts"); 

&startTranscriptAlignToContigs($mgr,"newTranscripts"); 

&copyFilesFromComputeCluster($mgr,"newTranscripts","repeatmask"); 

&copyFilesFromComputeCluster($mgr,"newTranscripts-contigs","genome"); 

&loadContigAlignments($mgr, "newTranscripts", "contigs");

&clusterByContigAlign($mgr, "initial");

&splitCluster("initial", $mgr);  

&assembleTranscripts("", $propertySet->getProp('reassemble'), "initial", $mgr); 

&reassembleTranscripts("initial", $mgr); 

&deleteAssembliesWithNoTranscripts($mgr, "initial");

&extractAssemblies($mgr,"intermedTranscriptCons");  
 
&copyFilesToComputeCluster($mgr,"intermedTranscriptCons"); 

&extractTranscriptSeqs($mgr,"unalignededTranscripts");

&copyFilesToComputeCluster($mgr,"unalignedtranscripts"); 

&startTranscriptMatrixOnComputeCluster($mgr,"intermed");

&copyFilesFromComputeCluster($mgr,"intermedTranscriptCons","matrix"); 

&clusterByBlastSim($mgr,"intermed","intermed-intermed","unaligned-unaligned","intermed-unaligned");

&splitCluster($mgr,"intermed"); 

&assembleTranscripts("--assemble_old", "no", "intermed", $mgr);

&reassembleTranscripts("intermed", $mgr); 

&deleteAssembliesWithNoTranscripts($mgr, "intermed");

&extractAssemblies($mgr,"finalTranscriptCons"); 

&copyFilesToComputeCluster($mgr,"finalTranscriptCons"); 

&startTranscriptAlignToContigs($mgr,"finalTranscriptCons"); 

&copyFilesFromComputeCluster($mgr,"finalTranscriptCons-contigs", "genome"); 

&loadContigAlignments($mgr, "finalTranscripts", "contigs"); 


$mgr->goodbye("Pipeline complete!\n");