adding things to check for dependencies

Author: mshakya

src/runPhaME

@@ -8,6 +8,7 @@ use lib "$Bin";
 use lib "$RealBin/../lib";
 use lib "$RealBin/../ext/lib/perl5";
 use File::Basename;
+use Time::Piece;
 use PhaME;
 use Cwd;
 
@@ -49,13 +50,20 @@ AUTHORS
    Los Alamos National Laboratory
 =cut
 
+#...............................................................................
+# global variables
+my $PACKAGENAME    = "PhaME";
+my $PACKAGEVERSION = "1.0.0";
+my $AUTHORS        = "Migun Shakya, Chienchi Lo, Sanaa Ahmed";
+my $URL            = 'https://github.com/LANL-Bioinformatics/PhaME';
+my $vcheck         = '';
 my $refdir;     # variable storing directory with reference sequence
 my $workdir;    # variable storing directory where all analysis will be done
 my $outdir;
 my $project;
 my $rsignal = 0;
 my $reference;
-my $aligner="bowtie";
+my $aligner = "bowtie";
 my $name;
 my $path;
 my $suffix;
@@ -91,17 +99,80 @@ my $mappingGaps;
 my $ptree;
 my $buildSNPdb = 0;
 my $message;
-my $PACKAGENAME="PhaME";
-my $PACKAGEVERSION="1.0.0";
 my $bindir = getBinDirectory();
 
+#...............................................................................
+# command line options
+
 GetOptions(
+    'vcheck'    => sub {check_version()},
     'version|v' => sub { version() },
-    'help|h' => sub { printusage() },
+    'help|h'    => sub { printusage() }
+
 );
 
+if ( !@ARGV ) {
+    print(@ARGV);
+    print "$0: Argument required.\n";
+    print "For help message use:\n";
+    print "runPhaME -h.\n";
+    exit 1;
+}
+
 my $control = $ARGV[0] || "phame.ctl";
-##########################################################################################
+
+#...............................................................................
+#check for depenencies
+
+sub parse_version {
+
+    # from snippy
+    my ( $cmd, $min, $re ) = @_;
+    open my $ver, '-|', $cmd . ' 2>&1'
+        or err ("Could not open pipe to '$cmd'");
+    my $blob = join '', <$ver>;
+        err ("Could not read output of '$cmd'") unless $blob;
+
+    #msg("parse=[$blob]");
+    $blob =~ $re;
+    $ver = defined $1 ? $1 : 0;
+        err ("Need $cmd >= $min but you have $ver - please upgrade it.")
+        if $ver < $min;
+    msg("Checking version: $cmd is >= $min - ok, have $ver");
+    return $ver;
+}
+
+sub check_version {
+# quit now if --vcheck was provided
+    parse_version( 'samtools --version', 1.3,   qr/samtools\s(\d+\.\d+)/ms );
+    parse_version( 'bcftools --version', 1.3,   qr/bcftools\s(\d+\.\d+)/ms );
+    parse_version( 'nucmer --version',   3.1,   qr/version\s(\d+\.\d+)/ms );
+    parse_version( 'bowtie2 --version',  2.3,   qr/version\s(\d+\.\d+)/ms );
+    parse_version( 'bwa',                0.7,   qr/Version:\s(\d+\.\d+)/ms );
+    parse_version( 'FastTree',           2.1,   qr/version\s(\d+\.\d+)/ms );
+    parse_version( 'bbmap.sh -v',        38.06, qr/Version\s(\d+\.\d+)/ms );
+    parse_version( 'raxmlHPC-PTHREADS -version', 8.2, qr/version\s(\d+\.\d+)/ms );
+    msg("Dependences look good!");
+    exit(0);
+}
+
+#----------------------------------------------------------------------
+
+sub msg {
+    my $t    = localtime;
+    my $line = "[" . $t->hms . "] @_\n";
+    print STDERR $line;
+}
+
+#----------------------------------------------------------------------
+
+sub err {
+    msg(@_);
+    exit(2);
+}
+
+#...............................................................................
+
 ## Read in control file
 open( CTL, "$control" ) || die "Please provide a control file";
 
@@ -124,16 +195,18 @@ while (<CTL>) {
     if (/project\s*=\s*(\S+)\s*#{0,1}.*$/) { $project = $1; }
 
     if (/reference\s*=\s*(0|1|2)\s*#{0,1}.*$/) { $rsignal = $1; }
-    if (/aligner\s*=\s*(\S+)\s*#{0,1}.*$/){$aligner=$1;}
+    if (/aligner\s*=\s*(\S+)\s*#{0,1}.*$/)     { $aligner = $1; }
     if ( $rsignal == 1 && /reffile\s*=\s*(\S+)\s*#{0,1}.*$/ ) {
         $reference = "$refdir/$1";
     }
-    elsif($rsignal==0){
-      opendir(DIR, $refdir);
-      my @reffiles = grep { /.[fna|fa|fasta|fsa]$/ && -f "$refdir/$_" } readdir(DIR);
-      $reference= "$refdir/". $reffiles[int(rand(scalar(@reffiles)))];
-      closedir DIR;
-   }
+    elsif ( $rsignal == 0 ) {
+        opendir( DIR, $refdir );
+        my @reffiles
+            = grep { /.[fna|fa|fasta|fsa]$/ && -f "$refdir/$_" } readdir(DIR);
+        $reference
+            = "$refdir/" . $reffiles[ int( rand( scalar(@reffiles) ) ) ];
+        closedir DIR;
+    }
 
     if (/cdsSNPS\s*=\s*(0|1)\s*#{0,1}.*$/) { $gsignal = $1; }
 
@@ -214,7 +287,6 @@ elsif ( $rsignal == 1 ) {
 
 ( $name, $path, $suffix ) = fileparse( "$reference", qr/\.[^.]*/ );
 
-
 print("\n");
 &print_timeInterval( "\n$runtime\n", "Loading information\n" );
 print "\tRefd:\t$refdir\n";
@@ -226,18 +298,17 @@ if ( !-d $refdir || !-d $workdir || !-d $outdir ) {
 }
 
 print "\tReference:\t$reference\n";
-if ( !-e "$reference" )
-    {print "File $reference does not exist.\n";
+if ( !-e "$reference" ) {
+    print "File $reference does not exist.\n";
     exit;
-    }
-
+}
 
 if ( $gsignal == 1 ) {
     if ( -e "$refdir/$name.gff" ) {
         $annotation = "$refdir/$name.gff";
         print "\tAnnotation:\t$annotation\n";
     }
-    elsif (-e "$refdir/$name.gff3" ) {
+    elsif ( -e "$refdir/$name.gff3" ) {
         $annotation = "$refdir/$name.gff3";
         print "\tAnnotation:\t$annotation\n";
     }
@@ -257,11 +328,11 @@ END_MESSAGE
 }
 
 if ( $pselection > 0 ) {
-    if ( -e "$refdir/$name.gff" ){
+    if ( -e "$refdir/$name.gff" ) {
         $genefile = "$refdir/$name.gff";
         print "\tGenes:\t$genefile\n";
     }
-    elsif ( -e "$refdir/$name.gff3" ){
+    elsif ( -e "$refdir/$name.gff3" ) {
         $genefile = "$refdir/$name.gff3";
         print "\tGenes:\t$genefile\n";
     }
@@ -519,7 +590,7 @@ if ( $check == 0 ) {
                 $contig_list{$list} = $genome_size;
             }
         }
-        if ( $read_mapping == 1 )  {
+        if ( $read_mapping == 1 ) {
             if (   $files =~ /.+\.f{1}a?s?t?q$/
                 && $files !~ /.+\.f{1}n|s?a?s?t?a$/
                 && $files !~ /.+\.contig$|\.contigs$|\.ctg$]$/ )
@@ -620,16 +691,20 @@ if ( $read_mapping == 1 ) {
             "map", $project );
         PhaME::removeGaps( $bindir, $reference, $mappingGaps );
         &print_timeInterval( $runtime, "Mapping reads to reference\n" );
-        my $end = PhaME::readsMapping( $workdir, $bindir,
-            "$workdir/reads_list.txt", $threads, $name, $error, $aligner, $logfile );
+        my $end
+            = PhaME::readsMapping( $workdir, $bindir,
+            "$workdir/reads_list.txt", $threads, $name, $error, $aligner,
+            $logfile );
         &print_timeInterval( $runtime, "$end\n" );
     }
     elsif ( $time == 1 ) {
         my $tempdir = $outdir . '/temp/';
         `mkdir -p $tempdir; cp $reference $tempdir`;
         &print_timeInterval( $runtime, "Mapping reads to reference\n" );
-        my $end = PhaME::readsMapping( $workdir, $bindir,
-            "$workdir/reads_list.txt", $threads, $name, $error, $aligner, $logfile );
+        my $end
+            = PhaME::readsMapping( $workdir, $bindir,
+            "$workdir/reads_list.txt", $threads, $name, $error, $aligner,
+            $logfile );
         &print_timeInterval( $runtime, "$end\n" );
     }
 }
@@ -638,7 +713,7 @@ if ( $buildSNP == 1 ) {
     &print_timeInterval( $runtime, "Identifying SNPs\n" );
     &print_timeInterval( $runtime, "Starting with gaps\n" );
     PhaME::identifyGaps( $outdir, "$workdir/working_list.txt", $name, "snp",
-    $project );
+        $project );
     &print_timeInterval( $runtime, "Gap identification complete\n" );
     if ( $gsignal == 1 ) {
         &print_timeInterval( $runtime, "Preparing to identify SNPs\n" );
@@ -654,31 +729,30 @@ if ( $buildSNP == 1 ) {
         "$workdir/working_list.txt", $project, $gsignal, $error, $logfile,
         $cutoff );
     if ( $gsignal == 1 ) {
-        print 
-            "\tSNPs from contigs and/or raw reads will be parsed\n";
-        print
-            "\tto synonymous and non-synonymous if given\n\n";
+        print "\tSNPs from contigs and/or raw reads will be parsed\n";
+        print "\tto synonymous and non-synonymous if given\n\n";
         my ( $genname, $genpath, $gensuffix )
             = fileparse( "$annotation", qr/\.[^.]*/ );
-        my $cds_gff = $outdir . "/$genname\_cds.gff";
+        my $cds_gff     = $outdir . "/$genname\_cds.gff";
         my $snps_folder = $outdir . "/snps";
-        my $ref_fasta = "$workdir/files/$genname.fna";
-        PhaME::SNPsAnalysis($cds_gff, $snps_folder, $ref_fasta, $logfile, $error);
+        my $ref_fasta   = "$workdir/files/$genname.fna";
+        PhaME::SNPsAnalysis( $cds_gff, $snps_folder, $ref_fasta, $logfile,
+            $error );
     }
-    
+
     &print_timeInterval( $runtime, "$end\n" );
 }
 
 if ( $buildtree == 1 || $bs == 1 ) {
-    &print_timeInterval($runtime, "Preparing all SNP phylogeny\n");
+    &print_timeInterval( $runtime, "Preparing all SNP phylogeny\n" );
     my $end = PhaME::buildTree( $bindir, $outdir, $threads, $tree,
         "$project\_all", $error, $logfile );
-    &print_timeInterval( $runtime, "DONE\n");
+    &print_timeInterval( $runtime, "DONE\n" );
     if ( $gsignal == 1 ) {
-        &print_timeInterval( $runtime, "Preparing CDS phylogeny\n");
+        &print_timeInterval( $runtime, "Preparing CDS phylogeny\n" );
         PhaME::buildTree( $bindir, $outdir, $threads, $tree, "$project\_cds",
             $error, $logfile );
-        &print_timeInterval( $runtime, "DONE\n");
+        &print_timeInterval( $runtime, "DONE\n" );
     }
     &print_timeInterval( $runtime, "$end\n" );
     if ( $bsignal == 1 ) {
@@ -854,13 +928,13 @@ sub version {
 }
 
 sub printusage {
-   print "\n$PACKAGENAME (version $PACKAGEVERSION)\n";
-   print "\nUSAGE: runPhaME <control file>\n\n";
-   print "-h show this help message and exit\n";
-   print "-v show version number and exit\n";
-   exit;
-   print "\n";
-   print "\n";
+    print "\n$PACKAGENAME (version $PACKAGEVERSION)\n";
+    print "\nUSAGE: runPhaME <control file>\n\n";
+    print "-h show this help message and exit\n";
+    print "-v show version number and exit\n";
+    print "--vcheck checks if all depenencies are correct and in path.\n";
+    exit;
+    print "\n";
+    print "\n";
 }
 
-