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1 #!/usr/bin/perl
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2 # bamqc_wrapper.pl
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3 # Joachim Jacob - joachim.jacob@gmail.com - 2013
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4
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5 use strict;
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6 use File::Temp 'tempdir';
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7 use File::Basename;
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8 use Log::Log4perl qw(:easy);
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9
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10 # ---------------------- Prepping Logging -----------------------------#
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11 ########################################################################
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12 # Log levels: $DEBUG $INFO $WARN $ERROR $FATAL
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13 # ConversionPattern: %d %-5p %F{1} [%M] (line %L): %m%n%n
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14 my $log_conf = q/
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15 log4perl.category = ERROR, Screen
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16 log4perl.appender.Screen.stderr=1
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17 log4perl.appender.Screen.layout=Log::Log4perl::Layout::PatternLayout
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18 log4perl.appender.Screen.layout.ConversionPattern = %d %-5p %m%n
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19 log4perl.appender.Screen = Log::Log4perl::Appender::Screen
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20 /;
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21
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22 Log::Log4perl::init( \$log_conf );
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23 my $logger = get_logger();
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24
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25 # ----------------- Getting parameters file ---------------------------#
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26 ########################################################################
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27 my ($configfile) = @ARGV;
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28 my (%para);
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29 open(CONFIG,"<$configfile");
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30 while (<CONFIG>) {
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31 if (/(\S+)==(.+)$/){ $para{ $1 } = $2 ; }
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32 }
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33 close(CONFIG);
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34
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35 =Excerpt Config parameters
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36
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37 ## first we pass some galaxy environment variables
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38 galtemp==${__new_file_path__}
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39
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40 bam==$bam
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41 c==$c
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42 hm==$hm
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43 nr==$nr
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44 #if $customgtf.upload=="yes"
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45 gff==$customgtf.gff
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46 os==$customgtf.os
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47 p==$customgtf.p
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48 #end if
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49
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50 =cut
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51
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52 for my $para (keys %para){
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53 INFO "$para\tset to\t$para{$para}";
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54 }
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55
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56
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57 # ---------------------- Prepping temp dir ----------------------------#
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58 ########################################################################
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59 # within the temporary directory of Galaxy, we create a temporary dir
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60
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61 my $galtemp = $para{'galtemp'};
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62 DEBUG "\nReceived Galaxy temporary directory:\n$galtemp";
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63
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64 my $tempdir = File::Temp->tempdir('tmpXXXXX', DIR => $galtemp, CLEANUP => 1);
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65 mkdir "$tempdir", 077 unless -d "$tempdir";
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66 INFO "\nTemporary directory:\n$tempdir";
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67
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68
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69 # ---------------------- Output files ---------------------------------#
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70 ########################################################################
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71 # Two possible scenarios
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72 # - output is written to the file at the output location in config file
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73 # - output is moved to the output file location
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74
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75 # open (SAMOUTPUT, ">$para{'output_sam'}")
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76 # or ( ERROR "Could not open output file for writing! (file:$para{'output_sam'}" and die );
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77 # print SAMOUTPUT "Here comes sam\n";
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78 # close (SAMOUTPUT);
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79
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80
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81 # -------------------- Assembling command ----------------------------#
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82 ########################################################################
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83 my $outdir="bamqc_output";
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84 my $qualimap_path=""; # for tool_dependency later on
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85 my $command = $qualimap_path."qualimap bamqc --outdir $outdir"; # this will ultimately be executed
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86
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87 # based on parameters, which are called by $para{'parametername'}
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88 # the command is assembled
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89 $command .= " -bam $para{'bam'} -hm $para{'hm'} -nr $para{'nr'}";
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90 if($para{'c'}){$command .= " $para{'c'} "; }
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91 if ( $para{'gff'} ){
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92 $command .= " -gff $para{'gff'} -p $para{'p'} ";
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93 if($para{'os'}) {
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94 $command .= $para{'os'};
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95 }
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96 }
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97
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98 $command .= " -nt 4 -outformat HTML";
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99
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100
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101 # --------------------- Executing command ----------------------------#
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102 ########################################################################
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103 run_process($command, "qualimap bamqc", ".");
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104
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105
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106 # ----------------- Postprocessing command ---------------------------#
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107 ########################################################################
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108 # Hackish !!
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109
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110 my $librarydir = dirname($para{'bamqc_result'});
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111 my $jobworkdir = dirname($para{'outputdir'});
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112 my $files_path_name = basename($para{'outputdir'});
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113 INFO "\n Librarydir = $librarydir \n jobworkdir = $jobworkdir \n files_path_name = $files_path_name \n";
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114 system("mv $jobworkdir/bamqc_output $librarydir/$files_path_name") == 0 or die "Could not move output data to $librarydir\n";
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115 system("rm -rf $para{'bamqc_result'}") == 0 or die "Could not post-process the results...\n";
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116 system("ln -s $librarydir/$files_path_name/qualimapReport.html $para{'bamqc_result'}") == 0 or die "Could not move output data to $librarydir\n";
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117
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118
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119 # --------------------------- Exiting --------------------------------#
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120 ########################################################################
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121 exit 0;
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122
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123
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124
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125 ### Subroutines ###
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126 ########################################################################
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127 sub run_process {
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128 my ($command, $name, $tempdir)= @_;
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129 my $logger = get_logger();
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130 INFO "\nProcess to launch:\n $command\nIn directory\n$tempdir\n";
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131 system("cd $tempdir; $command 2>/dev/null") == 0 or die "$name failed\nExit status $?\nCommand: $command";
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132 if ($? == -1) {
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133 print "failed to execute: $!\n";
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134 } elsif ($? & 127) {
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135 printf "child died with signal %d, %s coredump\n", ($? & 127), ($? & 128) ? 'with' : 'without';
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136 } else {
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137 printf "$name executed successfully\n", $? >> 8;
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138 }
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139 }
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140
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141
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142
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