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1 #!/usr/bin/perl
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2
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3 =head1 NAME
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4 install.pl
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5
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6 =head1 SYNOPSIS
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7 USAGE: install.pl --prefix=/location/of/install/dir
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8
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9 =head1 OPTIONS
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10
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11 B<--prefix, -p>
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12 Required. Prefix location where package will be installed.
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13
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14 B<--perl_exec, -e>
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15 Optional. If perl exec is other than /usr/bin/perl please specify location of perl install
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16
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17 B<--help,-h>
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18
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19
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20 =head1 DESCRIPTION
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21 Install package
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22
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23 =head1 INPUT
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24
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25 =head1 OUTPUT
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26
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27
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28 =head1 CONTACT
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29 bjaysheel@gmail.com
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30
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31
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32 ==head1 EXAMPLE
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33 ./install.pl --prefix=/prefix
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34
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35 =cut
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36
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37 use strict;
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38 use warnings;
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39 use Cwd;
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40 use Data::Dumper;
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41 use Pod::Usage;
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42 use Getopt::Long qw(:config no_ignore_case no_auto_abbrev pass_through);
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43
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44 my %options = ();
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45 my $results = GetOptions (\%options,
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46 'prefix|p=s',
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47 'perl_exec|e=s',
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48 'help|h') || pod2usage();
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49
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50 ## display documentation
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51 if( $options{'help'} ){
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52 pod2usage( {-exitval => 0, -verbose => 2, -output => \*STDERR} );
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53 }
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54
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55 #############################################################################
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56 #### make sure everything passed was peachy
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57 &check_parameters(\%options);
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58
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59 #### print time now.
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60 timestamp();
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61
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62 my $this = {};
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63 my $progress = {};
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64 my $cmd = "";
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65
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66 #### get current working dir
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67 $this->{source} = getcwd();
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68
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69 $progress = getProgress();
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70
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71 #### make logs dir
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72 $cmd = "mkdir -p $options{prefix}/logs";
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73 execute_cmd($cmd);
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74
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75 #### installling libraries required for successfull run
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76 install_libraries();
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77
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78 #### unpack binary dir containing all binary to be installed
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79 #### which are required for successfull run
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80 print STDERR "\n\nInstalling binaries...\n";
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81
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82 #### install each package in binary folder.
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83 my @packages = qw(stringApprox levD);
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84
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85 foreach my $tool (@packages) {
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86 if ((exists $progress->{$tool}) && ($progress->{$tool})){
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87 print STDERR "\t$tool already installed. Skipping...\n";
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88 } else {
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89 print STDERR "\tInstalling $tool...\n";
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90
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91 #### unpack and install each tool
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92 eval("install_${tool}()");
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93 }
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94 }
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95
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96 #### copy source code and update paths for perl and libs
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97 install_source();
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98
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99 #### completion message
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100 print "\n\n\tSoftSearch installation complete. Use following command to initiate a test run\n";
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101 print "\n\tperl $options{prefix}/src/SoftSearch.pl -f {GENOME} -b {BAM_FILE}\n\n";
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102
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103 #### print time now
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104 timestamp();
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105
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106 #############################################################################
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107 sub check_parameters {
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108 my $options = shift;
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109
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110 my @required = qw(prefix);
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111
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112 foreach my $key (@required) {
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113 unless ($options{$key}) {
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114 print STDERR "ARG: $key is required\n";
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115 pod2usage({-exitval => 2, -message => "error message", -verbose => 1, -output => \*STDERR});
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116 exit(-1);
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117 }
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118 }
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119
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120 $options{'perl_exec'} = "/usr/bin/perl" unless($options{'perl_exec'});
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121 }
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122
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123 #############################################################################
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124 sub getProgress {
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125 my $hash = {};
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126 my @sofar;
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127
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128 #### if file exists get progress so far.
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129 if (-s "$options{prefix}/progress.txt") {
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130 open(FHD, "<", "$options{prefix}/progress.txt") or die "Could not open file to read $options{prefix}/progress.txt";
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131 while(<FHD>){
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132 chomp $_;
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133 push @sofar, $_;
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134 }
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135 close(FHD);
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136
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137 map { $hash->{$1} = $2 if( /([^=]+)\s*=\s*([^=]+)/ ) } @sofar;
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138 }
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139
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140 #### return hash
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141 return $hash;
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142 }
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143
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144 #############################################################################
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145 sub setProgress {
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146 my $hash = shift;
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147
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148 open(OUT, ">", "$options{prefix}/progress.txt") or die "Could not open file to write $options{prefix}/progress.txt";
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149
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150 foreach my $key (keys %{$hash}){
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151 print OUT $key."=".$hash->{$key}."\n";
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152 }
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153
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154 close(OUT);
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155 }
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156
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157 #############################################################################
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158 sub install_libraries {
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159 if ((exists $progress->{libraries}) && ($progress->{libraries})){
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160 print STDERR "\tLibraries already installed. Skipping...\n";
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161 return;
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162 }
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163
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164 print STDERR "\n\nInstalling libraries...\n\n";
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165 chdir($this->{source});
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166
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167 $cmd = "cp -r $this->{source}/library $options{prefix}/lib";
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168 execute_cmd($cmd);
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169
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170 $progress->{libraries} = 1;
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171 setProgress($progress);
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172 }
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173
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174 #############################################################################
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175 sub install_stringApprox {
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176 #### check and install dir
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177 my $dir = "$options{prefix}/lib";
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178 my $cmd = "";
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179
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180 $cmd = "mkdir -p $dir";
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181 execute_cmd($cmd);
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182
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183 $cmd = "tar -zxvf $this->{source}/binary/String-Approx-3.27.tar.gz -C $this->{source}/binary";
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184 execute_cmd($cmd);
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185
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186 chdir("$this->{source}/binary/String-Approx-3.27");
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187 $cmd = "perl Makefile.PL INSTALL_BASE=$options{prefix}";
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188 $cmd .= " 1>$options{prefix}/logs/StringApprox.out";
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189 $cmd .= " 2>$options{prefix}/logs/StringApprox.err";
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190 execute_cmd($cmd);
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191
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192 $cmd = "make && make install";
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193 $cmd .= " 1>>$options{prefix}/logs/StringApprox.out";
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194 $cmd .= " 2>>$options{prefix}/logs/StringApprox.err";
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195 execute_cmd($cmd);
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196
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197 $cmd = "make install";
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198 $cmd .= " 1>>$options{prefix}/logs/StringApprox.out";
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199 $cmd .= " 2>>$options{prefix}/logs/StringApprox.err";
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200 execute_cmd($cmd);
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201
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202
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203 chdir("$this->{source}/binary");
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204 $cmd = "rm -rf $this->{source}/binary/String-Approx-3.27";
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205 execute_cmd($cmd);
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206
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207 $progress->{stringApprox} = 1;
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208 setProgress($progress);
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209 }
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210
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211 #############################################################################
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212 sub install_levD {
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213 #### check and install dir
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214 my $dir = "$options{prefix}/lib";
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215 my $cmd = "";
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216
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217 $cmd = "mkdir -p $dir";
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218 execute_cmd($cmd);
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219
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220 $cmd = "tar -zxvf $this->{source}/binary/Text-LevenshteinXS-0.03.tar.gz -C $this->{source}/binary";
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221 execute_cmd($cmd);
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222
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223 chdir("$this->{source}/binary/Text-LevenshteinXS-0.03");
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224 $cmd = "perl Makefile.PL INSTALL_BASE=$options{prefix}";
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225 $cmd .= " 1>$options{prefix}/logs/levD.out";
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226 $cmd .= " 2>$options{prefix}/logs/levD.err";
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227 execute_cmd($cmd);
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228
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229 $cmd = "make";
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230 $cmd .= " 1>>$options{prefix}/logs/levD.out";
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231 $cmd .= " 2>>$options{prefix}/logs/levD.err";
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232 execute_cmd($cmd);
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233
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234 $cmd .= "make install";
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235 $cmd .= " 1>>$options{prefix}/logs/levD.out";
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236 $cmd .= " 2>>$options{prefix}/logs/levD.err";
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237 execute_cmd($cmd);
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238
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239 chdir("$this->{source}/binary");
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240 $cmd = "rm -rf $this->{source}/binary/Text-LevenshteinXS-0.03";
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241 execute_cmd($cmd);
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242
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243 $progress->{levD} = 1;
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244 setProgress($progress);
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245 }
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246
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247 #############################################################################
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248 sub install_source {
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249 if ((exists $progress->{source}) && ($progress->{source})){
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250 print STDERR "\tSource already installed. Skipping...\n";
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251 return;
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252 }
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253
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254 print STDERR "\n\nInstalling source...\n\n";
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255
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256 #### create dir to store source code
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257 $cmd = "mkdir -p $options{prefix}/src";
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258 execute_cmd($cmd);
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259
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260 $cmd = "cp -r $this->{source}/script/* $options{prefix}/src/.";
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261 execute_cmd($cmd);
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262
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263 #### make sure all scripts are executable
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264 $cmd = "chmod -R +x $options{prefix}/src";
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265 execute_cmd($cmd);
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266
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267 #### replace /usr/local/biotools/perl/5.10.0/bin/perl with perl_exec
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268 $options{perl_exec} =~ s/\//\\\//g;
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269 $cmd = "find $options{prefix}/src -name \"*.pl\" -print";
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270 $cmd .= " -exec sed -i 's/#!\\/usr\\/local\\/biotools\\/perl\\/5.10.0\\/bin\\/perl/#!$options{perl_exec}/' {} \\;";
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271 execute_cmd($cmd);
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272
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273 #### check if perl exec location is other than /usr/bin/perl
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274 if ($options{perl_exec} !~ /^\/usr\/bin\/perl$/) {
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275 $cmd = "find $options{prefix}/src -name \"*.pl\" -print";
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276 $cmd .= " -exec sed -i 's/#!\\/usr\\/bin\\/perl/#!$options{perl_exec}/' {} \\;";
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277 execute_cmd($cmd);
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278 }
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279
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280 #### replace library references to local install
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281 my $lib = "$options{prefix}/lib";
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282 $lib =~ s/\//\\\//g;
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283
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284 $cmd = "find $options{prefix}/src -name \"*.pl\" -print";
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285 $cmd .= " -exec sed -i 's/\\/data2\\/bsi\\/reference\\/softsearch\\/lib/$lib/' {} \\;";
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286 execute_cmd($cmd);
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287
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288 $cmd = "find $options{prefix}/lib -name \"LevD.pm\" -print";
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289 $cmd .= " -exec sed -i 's/\\/data2\\/bsi\\/reference\\/softsearch\\/lib/$lib/' {} \\;";
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290 execute_cmd($cmd);
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291
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292 $progress->{source} = 1;
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293 setProgress($progress);
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294 }
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295
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296 #############################################################################
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297 sub execute_cmd {
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298 my $cmd = shift;
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299
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300 system($cmd);
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301
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302 #while (( $? >> 8 ) != 0 ){
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303 # print STDERR "ERROR: Following command failed to execute. Exiting execution of workflow\n$cmd\n";
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304 # exit(-1);
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305 #}
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306 }
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307
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308 #############################################################################
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309 sub timestamp {
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310 my @months = qw(Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec);
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311 my @weekDays = qw(Sun Mon Tue Wed Thu Fri Sat Sun);
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312 my ($second, $minute, $hour, $dayOfMonth, $month, $yearOffset, $dayOfWeek, $dayOfYear, $daylightSavings) = localtime();
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313 my $year = 1900 + $yearOffset;
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314 my $theTime = "$hour:$minute:$second, $weekDays[$dayOfWeek] $months[$month] $dayOfMonth, $year";
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315 print "Time now: " . $theTime."\n";
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316 }
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