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0
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1 #!/usr/bin/perl
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2
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3 use Getopt::Long;
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4 use LWP::Simple qw($ua getstore get);
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5 use File::Listing qw(parse_dir);
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6
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7 $| = 1;
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8 our $VERSION = 2.6;
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9
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10 # CONFIGURE
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11 ###########
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12
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13 my ($DEST_DIR, $ENS_CVS_ROOT, $API_VERSION, $BIOPERL_URL, $CACHE_URL, $help);
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14
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15 GetOptions(
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16 'DESTDIR|d=s' => \$DEST_DIR,
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17 'VERSION|v=i' => \$API_VERSION,
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18 'BIOPERL|b=s' => \$BIOPERL_URL,
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19 'CACHEURL|u=s' => \$CACHE_URL,
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20 'CACHEDIR|c=s' => \$CACHE_DIR,
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21 'HELP|h' => \$help
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22 );
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23
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24 if(defined($help)) {
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25 usage();
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26 exit(0);
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27 }
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28
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29 my $default_dir_used;
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30
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31 # check if $DEST_DIR is default
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32 if(defined($DEST_DIR)) {
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33 print "Using non-default installation directory $DEST_DIR - you will probably need to add $DEST_DIR to your PERL5LIB\n";
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34 $default_dir_used = 0;
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35 }
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36 else {
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37 $DEST_DIR ||= '.';
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38 $default_dir_used = 1;
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39 }
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40
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41 my $lib_dir = $DEST_DIR;
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42
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43 $DEST_DIR .= '/Bio';
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44 $ENS_CVS_ROOT ||= 'http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/';
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45 $BIOPERL_URL ||= 'http://bioperl.org/DIST/old_releases/bioperl-1.2.3.tar.gz';
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46 $API_VERSION ||= 68;
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47 $CACHE_URL ||= "ftp://ftp.ensembl.org/pub/release-$API_VERSION/variation/VEP";
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48 $CACHE_DIR ||= $ENV{HOME}.'/.vep';
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49
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50 our $prev_progress = 0;
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51
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52 print "\nHello! This installer is configured to install v$API_VERSION of the Ensembl API for use by the VEP.\nIt will not affect any existing installations of the Ensembl API that you may have.\n\nIt will also download and install cache files from Ensembl's FTP server.\n\n";
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53
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54
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55 # CHECK EXISTING
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56 ################
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57
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58 print "Checking for installed versions of the Ensembl API...";
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59
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60 # test if the user has the API installed
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61 my $has_api = {
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62 'ensembl' => 0,
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63 'ensembl-variation' => 0,
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64 'ensembl-functgenomics' => 0,
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65 };
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66
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67 eval q{
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68 use Bio::EnsEMBL::Registry;
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69 };
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70
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71 my $installed_version;
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72
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73 unless($@) {
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74 $has_api->{ensembl} = 1;
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75
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76 $installed_version = Bio::EnsEMBL::Registry->software_version;
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77 }
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78
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79 eval q{
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80 use Bio::EnsEMBL::Variation::Utils::VEP;
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81 };
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82
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83 $has_api->{'ensembl-variation'} = 1 unless $@;
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84
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85 eval q{
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86 use Bio::EnsEMBL::Funcgen::RegulatoryFeature;
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87 };
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88
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89 $has_api->{'ensembl-functgenomics'} = 1 unless $@;
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90
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91
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92 print "done\n";
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93
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94 my $total = 0;
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95 $total += $_ for values %$has_api;
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96
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97 my $message;
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98
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99 if($total == 3) {
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100
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101 if(defined($installed_version)) {
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102 if($installed_version == $API_VERSION) {
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103 $message = "It looks like you already have v$API_VERSION of the API installed.\nYou shouldn't need to install the API";
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104 }
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105
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106 elsif($installed_version > $API_VERSION) {
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107 $message = "It looks like this installer is for an older distribution of the API than you already have";
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108 }
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109
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110 else {
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111 $message = "It looks like you have an older version (v$installed_version) of the API installed.\nThis installer will install a limited set of the API v$API_VERSION for use by the VEP only";
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112 }
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113 }
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114
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115 else {
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116 $message = "It looks like you have an unidentified version of the API installed.\nThis installer will install a limited set of the API v$API_VERSION for use by the VEP only"
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117 }
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118 }
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119
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120 elsif($total > 0) {
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121 $message = "It looks like you already have the following API modules installed:\n\n".(join "\n", grep {$has_api->{$_}} keys %$has_api)."\n\nThe VEP requires the ensembl, ensembl-variation and optionally ensembl-functgenomics modules";
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122 }
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123
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124 if(defined($message)) {
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125 print "$message\n\nAre you sure you want to continue installing the API (y/n)? ";
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126
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127 my $ok = <>;
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128
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129 if($ok !~ /^y/i) {
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130 print " - skipping API installation\n";
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131 goto CACHE;
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132 }
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133 }
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134
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135
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136
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137 # SETUP
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138 #######
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139
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140 print "\nSetting up directories\n";
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141
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142 # check if install dir exists
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143 if(-e $DEST_DIR) {
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144 print "Destination directory $DEST_DIR already exists.\nDo you want to overwrite it (if updating VEP this is probably OK) (y/n)? ";
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145
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146 my $ok = <>;
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147
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148 if($ok !~ /^y/i) {
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149 print "Exiting\n";
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150 exit(0);
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151 }
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152
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153 else {
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154 unless($default_dir_used) {
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155 print "WARNING: You are using a non-default install directory.\nPressing \"y\" again will remove $DEST_DIR and its contents!!!\nAre you really, really sure (y/n)? ";
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156 $ok = <>;
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157
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158 if($ok !~ /^y/i) {
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159 print "Exiting\n";
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160 exit(0);
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161 }
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162 }
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163
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164 # try to delete the existing dir
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165 `rm -rf $DEST_DIR`;
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166 }
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167 }
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168
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169 mkdir($DEST_DIR) or die "ERROR: Could not make directory $DEST_DIR\n";
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170 mkdir($DEST_DIR.'/tmp') or die "ERROR: Could not make directory $DEST_DIR/tmp\n";
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171
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172 # set up a user agent's proxy
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173 $ua->env_proxy;
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174
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175 # enable progress
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176 eval q{
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177 $ua->show_progress(1);
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178 };
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179
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180
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181
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182 # API
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183 #####
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184
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185 print "\nDownloading required files\n";
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186
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187 # set up the URLs
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188 my $ensembl_url_tail = '.tar.gz?root=ensembl&view=tar&only_with_tag=branch-ensembl-';
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189
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190 foreach my $module(qw(ensembl ensembl-variation ensembl-functgenomics)) {
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191 my $url = $ENS_CVS_ROOT.$module.$ensembl_url_tail.$API_VERSION;
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192
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193 print " - fetching $module\n";
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194
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195 my $target_file = $DEST_DIR.'/tmp/'.$module.'.tar.gz';
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196
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197 unless(getstore($url, $target_file) == 200) {
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198 die "ERROR: Failed to fetch $module from $url - perhaps you have a proxy/firewall? Set the http_proxy ENV variable if you do\nError code: $response\n";
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199 }
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200
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201 print " - unpacking $target_file\n";
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202 unpack_tar("$DEST_DIR/tmp/$module.tar.gz", "$DEST_DIR/tmp/");
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203
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204 print " - moving files\n";
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205
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206 if($module eq 'ensembl') {
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207 `mv -f $DEST_DIR/tmp/$module/modules/Bio/EnsEMBL $DEST_DIR/`;
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208 }
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209 elsif($module eq 'ensembl-variation') {
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210 `mv -f $DEST_DIR/tmp/$module/modules/Bio/EnsEMBL/Variation $DEST_DIR/EnsEMBL/`;
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211 }
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212 elsif($module eq 'ensembl-functgenomics') {
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213 `mv -f $DEST_DIR/tmp/$module/modules/Bio/EnsEMBL/Funcgen $DEST_DIR/EnsEMBL/`;
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214 }
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215
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216 `rm -rf $DEST_DIR/tmp/$module`;# or die "ERROR: Failed to remove directory $DEST_DIR/$module\n";
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217 }
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218
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219
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220
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221 # BIOPERL
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222 #########
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223
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224 # now get BioPerl
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225 print " - fetching BioPerl\n";
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226
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227 $bioperl_file = (split /\//, $BIOPERL_URL)[-1];
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228
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229 my $target_file = $DEST_DIR.'/tmp/'.$bioperl_file;
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230
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231 unless(getstore($BIOPERL_URL, $target_file) == 200) {
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232 die "ERROR: Failed to fetch BioPerl from $BIOPERL_URL - perhaps you have a proxy/firewall?\nError code: $response\n";
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233 }
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234
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235 print " - unpacking $target_file\n";
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236 unpack_tar("$DEST_DIR/tmp/$bioperl_file", "$DEST_DIR/tmp/");
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237
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238 print " - moving files\n";
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239
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240 $bioperl_file =~ /(bioperl.+?)\.tar\.gz/;
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241 my $bioperl_dir = $1;
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242 `mv -f $DEST_DIR/tmp/$bioperl_dir/Bio/* $DEST_DIR/`;
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243 `rm -rf $DEST_DIR/tmp/$bioperl_dir`;# or die "ERROR: Failed to remove directory $DEST_DIR/$bioperl_dir\n";
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244 `rm -rf $DEST_DIR/tmp`;
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245
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246
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247
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248 # TEST
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249 ######
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250
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251 print "\nTesting VEP script\n";
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252
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253 my $test_vep = `perl variant_effect_predictor.pl --help 2>&1`;
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254
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255 $test_vep =~ /ENSEMBL VARIANT EFFECT PREDICTOR/ or die "ERROR: Testing VEP script failed with the following error\n$test_vep\n";
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256
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257 print " - OK!\n";
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258
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259
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260
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261 # CACHE FILES
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262 #############
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263
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264 CACHE:
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265
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266 print "\nThe VEP can either connect to remote or local databases, or use local cache files.\n";
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267 print "Cache files will be stored in $CACHE_DIR\n";
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268 print "Do you want to install any cache files (y/n)? ";
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269
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270 my $ok = <>;
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271
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272 if($ok !~ /^y/i) {
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273 print "Exiting\n";
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274 exit(0);
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275 }
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276
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277 # check cache dir exists
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278 if(!(-e $CACHE_DIR)) {
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279 print "Cache directory $CACHE_DIR does not exists - do you want to create it (y/n)? ";
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280
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281 my $ok = <>;
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282
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283 if($ok !~ /^y/i) {
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284 print "Exiting\n";
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285 exit(0);
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286 }
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287
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288 mkdir($CACHE_DIR) or die "ERROR: Could not create directory $CACHE_DIR\n";
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289 }
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290
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291 mkdir($CACHE_DIR.'/tmp') unless -e $CACHE_DIR.'/tmp';
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292
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293 # get list of species
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294 print "\nDownloading list of available cache files\n";
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295
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296 my $num = 1;
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297 my $species_list;
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298 my @files;
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299 push @files, map {$_->[0]} grep {$_->[0] =~ /tar.gz/} @{parse_dir(get($CACHE_URL))};
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300
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301 # if we don't have a species list, we'll have to guess
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302 if(!scalar(@files)) {
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303 print "Could not get current species list - using predefined list instead\n";
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304
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305 @files = (
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306 "bos_taurus_vep_$API_VERSION.tar.gz",
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307 "danio_rerio_vep_$API_VERSION.tar.gz",
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308 "homo_sapiens_vep_$API_VERSION.tar.gz",
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309 "homo_sapiens_vep_$API_VERSION\_sift_polyphen.tar.gz",
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310 "mus_musculus_vep_$API_VERSION.tar.gz",
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311 "rattus_norvegicus_vep_$API_VERSION.tar.gz",
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312 );
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313 }
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314
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315 foreach my $file(@files) {
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316 $species_list .= $num++." : ".$file."\n";
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317 }
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318
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319 print "The following species/files are available; which do you want (can specify multiple separated by spaces): \n$species_list\n? ";
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320
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321 foreach my $file(split /\s+/, <>) {
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322 my $file_path = $files[$file - 1];
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323
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324 my ($species, $file_name);
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325
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326 if($file_path =~ /\//) {
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327 ($species, $file_name) = (split /\//, $file_path);
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328 }
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329 else {
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330 $file_name = $file_path;
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331 $file_name =~ m/^(\w+?\_\w+?)\_vep/;
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332 $species = $1;
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333 }
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334
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335 # check if user already has this species and version
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336 if(-e "$CACHE_DIR/$species/$API_VERSION") {
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337 print "\nWARNING: It looks like you already have the cache for $species (v$API_VERSION) installed.\nIf you continue the existing cache will be overwritten.\nAre you sure you want to continue (y/n)? ";
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338
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339 my $ok = <>;
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340
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341 if($ok !~ /^y/i) {
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342 print " - skipping $species\n";
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343 next;
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344 }
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345
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346 `rm -rf $CACHE_DIR/$species/$API_VERSION`;
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347 }
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348
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349 my $target_file = "$CACHE_DIR/tmp/$file_name";
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350
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351 print " - downloading $CACHE_URL/$file_path\n";
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352
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353 unless(getstore("$CACHE_URL/$file_path", $target_file) == 200) {
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354 die "ERROR: Failed to fetch cache file $file_name from $CACHE_URL/$file_path - perhaps you have a proxy/firewall? Set the http_proxy ENV variable if you do\nError code: $response\n";
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355 }
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356
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357 print " - unpacking $file_name\n";
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358
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359 unpack_tar($target_file, $CACHE_DIR.'/tmp/');
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360
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361 # does species dir exist?
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362 if(!-e "$CACHE_DIR/$species") {
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363 mkdir("$CACHE_DIR/$species") or die "ERROR: Could not create directory $CACHE_DIR/$species\n";
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364 }
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365
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366 # move files
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367 `mv -f $CACHE_DIR/tmp/$species/$API_VERSION $CACHE_DIR/$species/`;
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368 }
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369
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370 # cleanup
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371 `rm -rf $CACHE_DIR/tmp`;
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372
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373 print "\nSuccess\n";
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374
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375
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376 # SUBS
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377 ######
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378
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379 # unpack a tarball with progress
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380 sub unpack_tar {
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381 my ($file, $dir) = @_;
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382
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383 my $count = 0;
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384
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385 open COUNT, "tar -tzvf $file 2>&1 |";
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386 $count++ while(<COUNT>);
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387 close COUNT;
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388
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389 my $i = 0;
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390 open EXTRACT, "tar -C $dir -xzvf $file 2>&1 |";
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391 progress($i++, $count) while(<EXTRACT>);
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392 close EXTRACT;
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393
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394 progress(1,1);
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395 $prev_progress = 0;
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396 print "\n";
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397
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398 `rm -rf $file`;
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399 }
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400
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401 # update or initiate progress bar
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402 sub progress {
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403 my ($i, $total) = @_;
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404
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405 my $width = 60;
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406 my $percent = int(($i/$total) * 100);
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407 my $numblobs = (($i/$total) * $width) - 2;
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408
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409 return unless $numblobs != $prev_progress;
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410 $prev_progress = $numblobs;
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411
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412 printf("\r% -${width}s% 1s% 10s", '['.('=' x $numblobs).($numblobs == $width - 2 ? '=' : '>'), ']', "[ " . $percent . "% ]");
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413 }
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414
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415 sub usage {
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416 my $usage =<<END;
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417 #---------------#
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418 # VEP INSTALLER #
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419 #---------------#
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420
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421 version $VERSION
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422
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423 By Will McLaren (wm2\@ebi.ac.uk)
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424
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425 http://www.ensembl.org/info/docs/variation/vep/vep_script.html#installer
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426
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427 Usage:
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428 perl INSTALL.pl [arguments]
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429
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430 Options
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431 =======
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432
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433 -h | --help Display this message and quit
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434 -d | --DESTDIR Set destination directory for API install (default = './')
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435 -v | --VERSION Set API version to install (default = 66)
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436 -c | --CACHEDIR Set destination directory for cache files (default = '$HOME/.vep/')
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437 END
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438
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439 print $usage;
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440 }
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