scripts/utilities/bp_netinstall.pl

   1 #!/usr/bin/perl
   2
   3 =head1 NAME
   4
   5 bp_netinstall.pl
   6
   7 =head1 SYNOPSIS
   8
   9   bp_netinstall.pl -b|--build_param_str BUILD_STRING [options]
  10
  11 options:
  12
  13  -h|--help                Show this message
  14  -d|--dev                 Use the development version of bioperl from git
  15  --build_param_str=<args> Parameters that are passed in at 'perl Build.PL'
  16  --install_param_str=<args>
  17                           Use this string to predefine './Build install'
  18                             parameters such as 'install_base' for
  19                             bioperl installation
  20  --bioperl_path           Path to BioPerl tarball (will not download BioPerl)
  21  --skip_start             Don't wait for 'Enter' at program start
  22
  23 =head1 DESCRIPTION
  24
  25 Net-based installer of BioPerl; this is based on the GBrowse netinstaller
  26 and hopefully all references to GBrowse have been removed.  Let me know if not.
  27
  28 Save this to disk as "bp_netinstall.pl" and run:
  29
  30    [sudo] perl bp_netinstall.pl
  31
  32 =head1 AUTHOR
  33
  34 Scott Cain scain@cpan.org
  35
  36 =head1 COPYRIGHT
  37
  38 2010. This script may be distributed under the same license as perl.
  39
  40 =cut
  41
  42
  43
  44 # Universal Net-based installer
  45 # Save this to disk as "bp_netinstall.pl" and run:
  46 #   perl bp_netinstall.pl
  47
  48 use warnings;
  49 use strict;
  50 use CPAN '!get';
  51 use Config;
  52 use Getopt::Long;
  53 use Pod::Usage;
  54 use File::Copy qw( cp move );
  55 use File::Temp qw(tempdir);
  56 use LWP::Simple;
  57 use Cwd;
  58
  59 use constant NMAKE => 'http://download.microsoft.com/download/vc15/patch/1.52/w95/en-us/nmake15.exe';
  60
  61 my ( $show_help, $get_from_cvs, $build_param_string, $working_dir,
  62      $get_bioperl_svn, $is_cygwin, $windows,
  63      $binaries, $make, $tmpdir, $bioperl_path,
  64      $skip_start, $install_param_string, $perl_path);
  65
  66 BEGIN {
  67
  68   GetOptions(
  69         'h|help'              => \$show_help,             # Show help and exit
  70         'd|dev'               => \$get_from_cvs,          # Use the dev svn
  71         'build_param_str=s'   => \$build_param_string,    # Build parameters
  72         'bioperl_dev'         => \$get_bioperl_svn,
  73         'bioperl_path=s'      => \$bioperl_path,
  74         'install_param_str=s' => \$install_param_string,
  75         'skip_start'          => \$skip_start,
  76         )
  77         or pod2usage(2);
  78   pod2usage(2) if $show_help;
  79
  80   $perl_path = $Config{perlpath};
  81
  82   print STDERR "\nAbout to install BioPerl and all its prerequisites.\n";
  83   print STDERR "\nYou will be asked various questions during this process. You can almost always";
  84   print STDERR "\naccept the default answer.\n";
  85   print STDERR "The whole process will take several minutes and will generate lots of messages.\n";
  86   print STDERR "\nPress return when you are ready to start!\n";
  87   my $h = <> unless $skip_start;
  88   print STDERR "*** Installing Perl files needed for a net-based install ***\n";
  89
  90   $windows = $Config{osname} =~ /mswin/i;
  91
  92
  93 # MAY not be necessary--we'll have to see.
  94 #  if ($windows and $] == 5.010) {
  95 #     print STDERR "\n\nActiveState Perl 5.10 is not compatible with GBrowse due to problems\n";
  96 #     print STDERR "with the AS implementation.  Please remove it and install Perl 5.8 instead.\n\n\n";
  97 #     exit(0);
  98 #  }
  99
 100 # Also MAY not be necessary
 101 #  if ($windows) {
 102 #     print STDERR "\n\nInstalling Win32 perl module\n\n";
 103 #     system("ppm install Win32");
 104 #  }
 105
 106   eval "CPAN::Config->load";
 107   eval "CPAN::Config->commit";
 108
 109   $working_dir = getcwd;
 110
 111   $tmpdir = tempdir(CLEANUP=>1)
 112     or die "Could not create temporary directory: $!";
 113
 114   $binaries = $Config{'binexp'};
 115   $make     = $Config{'make'};
 116
 117   if ($windows) {
 118     system("ppm install YAML");
 119   }
 120   else {
 121     CPAN::Shell->install('YAML');
 122   }
 123   CPAN::Shell->install('Archive::Zip');
 124   CPAN::Shell->install('HTML::Tagset');
 125   CPAN::Shell->install('LWP::Simple');
 126   eval "use Archive::Zip ':ERROR_CODES',':CONSTANTS'";
 127
 128   if ($windows && !-e "$binaries/${make}.exe") {
 129
 130     print STDERR "Installing make utility...\n";
 131     -w $binaries or die "$binaries directory is not writeable. Please re-login as Admin.\n";
 132     chdir $tmpdir;
 133
 134     my $rc = mirror(NMAKE,"nmake.zip");
 135     die "Could not download nmake executable from Microsoft web site."
 136       unless $rc == RC_OK() or $rc == RC_NOT_MODIFIED();
 137
 138     my $zip = Archive::Zip->new('nmake.zip') or die "Couldn't open nmake zip file for decompression: $!";
 139     $zip->extractTree == AZ_OK() or die "Couldn't unzip file: $!";
 140     -e 'NMAKE.EXE' or die "Couldn't extract nmake.exe";
 141
 142     cp('NMAKE.EXE',"$binaries/${make}.EXE") or die "Couldn't install nmake.exe: $!";
 143     cp('NMAKE.ERR',"$binaries/${make}.ERR"); # or die "Couldn't install nmake.err: $!"; # not fatal
 144   }
 145
 146   CPAN::Shell->install('Archive::Tar');
 147   #print STDERR $@;
 148   #print STDERR "at end of BEGIN{}\n";
 149   1;
 150 };
 151
 152 #print STDERR "here i am\n";
 153 #print STDERR $@;
 154
 155 use Archive::Tar;
 156 #use CPAN '!get';
 157
 158 $is_cygwin = 1 if ( $^O eq 'cygwin' );
 159
 160 if ($get_from_cvs) {
 161     $get_bioperl_svn = 1;
 162 }
 163
 164 #if ($wincvs or ($windows and $get_from_cvs)) {
 165 #    die "\n\nGBrowse is now in svn and fetching from svn on Windows\nis not currently supported\n ";
 166 #}
 167
 168 #if ($windows and !$wincvs and $get_gbrowse_cvs ) {
 169 #    die "\n\nThe development/cvs tags are not supported on Windows when\n"
 170 #        ."WinCVS is not installed; exiting...\n";
 171 #}
 172
 173 $build_param_string ||="";
 174 $install_param_string ||="";
 175
 176 use constant BIOPERL_VERSION      => 'BioPerl-1.6.1';
 177 use constant BIOPERL_REQUIRES     => '1.006001';  # sorry for the redundancy
 178 use constant BIOPERL_LIVE_URL     => 'http://github.com/bioperl/bioperl-live/tarball/master';
 179 use constant BIOPERL              => 'http://bioperl.org/DIST/'.BIOPERL_VERSION.'.tar.gz';
 180
 181 my %REPOSITORIES = (
 182                     #'BioPerl-Release-Candidates' => 'http://bioperl.org/DIST/RC',
 183                     'BioPerl-Regular-Releases'   => 'http://bioperl.org/DIST',
 184                     'Kobes'                      => 'http://theoryx5.uwinnipeg.ca/ppms',
 185                     'Bribes'                     => 'http://www.Bribes.org/perl/ppm',
 186                      'tcool'                     => 'http://ppm.tcool.org/archives/',
 187                     );
 188
 189
 190 # this is so that ppm can be called in a pipe
 191 $ENV{COLUMNS} = 80; # why do we have to do this?
 192 $ENV{LINES}   = 24;
 193
 194 setup_ppm() if $windows;
 195
 196 unless ( eval "use GD 2.31; 1" ) {
 197    if ($windows) {
 198      print STDERR "Installing GD via ppm.\n";
 199      print STDERR "(This may take a while...\n";
 200      system("ppm install GD");
 201   }
 202   else {
 203      print STDERR "Installing GD via CPAN...\n";
 204      CPAN::Shell->install('GD') unless eval "use GD 2.31; 1";
 205   }
 206 }
 207
 208 print STDERR "\n*** Installing prerequisites for BioPerl ***\n";
 209
 210 if ($windows and !eval "use DB_File; 1") {
 211   print STDERR "Installing DB_File for BioPerl.\n";
 212
 213   # GBrowse doesn't like DB_File 1.820, so we explicitly get DB_File by url
 214   system("ppm install http://ppm.tcool.org/archives/DB_File.ppd");
 215 }
 216 #system("ppm install SVG") if $windows;
 217 #CPAN::Shell->install('GD::SVG');
 218
 219 #needed?
 220 CPAN::Shell->install('IO::String');
 221 #CPAN::Shell->install('Text::Shellwords');
 222 #if ($windows) {
 223 #    #CGI::Session and Digest::MD5 both fail to install via cpan on windows
 224 #    system("ppm install CGI-Session");
 225 #    system("ppm install Digest-MD5");
 226 #}
 227 #else {
 228 #    CPAN::Shell->install('CGI::Session');
 229 #    CPAN::Shell->install('Digest::MD5');
 230 #}
 231 #CPAN::Shell->install('File::Temp');
 232 #CPAN::Shell->install('Class::Base');
 233 #CPAN::Shell->install('Statistics::Descriptive');
 234 #CPAN::Shell->install('Data::Stag');
 235
 236 my $version = BIOPERL_REQUIRES;
 237 if (!(eval "use Bio::Perl $version; 1") or $get_bioperl_svn or $bioperl_path) {
 238     print STDERR "\n*** Installing BioPerl ***\n";
 239
 240     #would like to use ppm, but ppm won't install 1.6
 241     #if ($windows and !$get_bioperl_svn and !$bioperl_path) {
 242     #  my $bioperl_index = find_bioperl_ppm();
 243     #  system("ppm install --force $bioperl_index");
 244     #} else {
 245         # recent versions of Module::Build fail to install without force!
 246         CPAN::Shell->force('Module::Build') unless eval "require Module::Build; 1";
 247         do_install(BIOPERL,
 248                    'bioperl.tgz',
 249                    BIOPERL_VERSION,
 250                    'Build',
 251                    $get_bioperl_svn ? 'svn' : '',
 252                    $build_param_string,
 253                    $bioperl_path,
 254                    $install_param_string,
 255                    $perl_path);
 256     #}
 257 }
 258 else {
 259     print STDERR "BioPerl is up to date.\n";
 260 }
 261
 262 print STDERR "\n *** Installing Bio::Graphics ***\n";
 263
 264
 265 #install biographics?
 266 CPAN::Shell->install('Bio::Graphics');
 267
 268 exit 0;
 269
 270 END {
 271   my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';
 272   open STDERR,">$null"; # windows has an annoying message when cleaning up temp file
 273 }
 274
 275 sub do_install {
 276   my ($download,$local_name,$distribution,$method,
 277          $from_cvs,$build_param_string,$file_path,$install_param_string,
 278          $perl_path) = @_;
 279
 280   $install_param_string ||= '';
 281   chdir $tmpdir;
 282
 283   do_get_distro($download,$local_name,$distribution,$from_cvs,$file_path);
 284
 285   my $build_str = $windows ? "Build" : "./Build";
 286
 287   if ($method eq 'make') {
 288       system("$perl_path Makefile.PL $build_param_string") == 0
 289             or die "Couldn't run perl Makefile.PL command\n";
 290       system("$make install UNINST=1 $install_param_string")    == 0 ;
 291   }
 292   elsif ($method eq 'Build') {
 293       system("$perl_path $build_str.PL --yes=1 $build_param_string")   == 0
 294             or die "Couldn't run perl Build.PL command\n";
 295       system("$build_str install --uninst 1 $install_param_string") == 0;
 296   }
 297 }
 298
 299 sub do_get_distro {
 300     my ($download,$local_name,$distribution,$distribution_method,$file_path) = @_;
 301
 302     if ($file_path) {
 303         chdir $working_dir;
 304         if (-e $file_path) { #must be an absolute path
 305             cp($file_path, "$tmpdir/$local_name");
 306         }
 307         elsif (-e "$working_dir/$file_path") { #assume it's a rel path from the original directory
 308             cp("$working_dir/$file_path", "$tmpdir/$local_name");
 309         }
 310         else {
 311             print "Couldn't find $file_path; nothing to do so quitting...\n";
 312             exit(-1);
 313         }
 314         $distribution = ($local_name =~ /gbrowse/)
 315                       ? "Generic-Genome-Browser" : "bioperl-live";
 316         chdir $tmpdir;
 317         extract_tarball($local_name,$distribution);
 318     }
 319     elsif ($distribution_method) {
 320         my $distribution_dir;
 321         print STDERR "Downloading bioperl-live...\n";
 322         $distribution_dir = 'bioperl-live';
 323
 324         my $filename = 'bioperl-live.tar.gz'; # =determine_filename();
 325         my $url = BIOPERL_LIVE_URL."/$filename";
 326
 327         my $rc = mirror($url, $filename);
 328         unless ($rc == RC_OK or $rc == RC_NOT_MODIFIED){
 329             print STDERR "Failed to get nightly bioperl-live file: $rc\n";
 330             return undef;
 331         }
 332         extract_tarball($filename,$distribution_dir);
 333         return 1;
 334         chdir $distribution_dir
 335             or die "Couldn't enter $distribution_dir directory: $@";
 336     }
 337     else {
 338         print STDERR "Downloading $download...\n";
 339         my $rc = mirror($download,$local_name);
 340         die "Could not download $distribution distribution from $download."
 341             unless $rc == RC_OK or $rc == RC_NOT_MODIFIED;
 342
 343         extract_tarball($local_name,$distribution);
 344     }
 345     return 1;
 346 }
 347
 348 #this is probably not going to be needed again, as the nightly
 349 #bioperl build names have been simplified
 350 sub determine_filename {
 351   my $listing = "dirlisting.html";
 352   my $rc = mirror(BIOPERL_LIVE_URL, $listing);
 353   die "Could not get directory listing of bioperl nightly build url: $rc\n"
 354       unless ($rc == RC_OK or $rc == RC_NOT_MODIFIED);
 355
 356   my $filename;
 357   open my $LIST, '<', $listing or die "Could not read file '$listing': $!\n";
 358   while (my $line = <$LIST>) {
 359     if ($line =~ /href="(bioperl-live.*?\.tar\.gz)"/) {
 360       $filename = $1;
 361       last;
 362     }
 363   }
 364   close $LIST;
 365   unlink $listing;
 366   return $filename;
 367 }
 368
 369 sub extract_tarball {
 370   my ($local_name,$distribution) = @_;
 371
 372   print STDERR "Unpacking $local_name...\n";
 373   my $z = Archive::Tar->new($local_name,1)
 374         or die "Couldn't open $distribution archive: $@";
 375   my @extracted = $z->extract()
 376         or die "Couldn't extract $distribution archive: $@";
 377
 378   if ($extracted[0]->{'name'} =~ /^(bioperl.*?)\//) {
 379     my $bioperl_dir = $1;
 380     move($bioperl_dir, $distribution) or die "couldn't move bioperl dir: $@";
 381   }
 382
 383   chdir $distribution
 384         or die "Couldn't enter $distribution directory: $@";
 385   return;
 386 }
 387
 388 # make sure ppm repositories are correct!
 389 sub setup_ppm {
 390   open my $S, "ppm repo list --csv|" or die "Could not open ppm for listing: $!\n";
 391   my %repository;
 392   while (my $line = <$S>) {
 393      chomp $line;
 394      my ($index, $package_count, $name) = split /,/, $line;
 395      $repository{$name} = $index;
 396   }
 397   close $S;
 398   print STDERR "Adding needed PPM repositories. This may take a while....\n";
 399   for my $name (keys %REPOSITORIES) {
 400      next if $repository{$name};
 401      system("ppm rep add $name $REPOSITORIES{$name}");
 402   }
 403 }
 404
 405 sub find_bioperl_ppm {
 406   print STDERR "Finding most recent bioperl...";
 407   open my $S,"ppm search bioperl |" or die "Could not open ppm for listing: $!\n";
 408   local $/ = ''; # paragraph mode
 409   my ($blessed_one, $blessed_version);
 410   my $best = 0;
 411   while (my $line = <$S>) {
 412     chomp $line;
 413     my ($number)     = ($line =~ /^(\d+): bioperl/m);
 414     my ($version)    = ($line =~ /^\s+Version: (.+)/m);
 415     my ($repository) = ($line =~ /^\s+Repo: (.+)/m);
 416     my $multiplier = 10000000;
 417     my $magnitude  = 0;
 418     # this dumb thing converts 1.5.1 into a real number
 419     foreach my $piece (split /[._]/, $version) {
 420       $magnitude += $piece * ($multiplier/=10);
 421     }
 422     ($blessed_one,$best,$blessed_version) = ($number,$magnitude,$version) if $best < $magnitude;
 423   }
 424   close $S;
 425   print STDERR $blessed_version ? "found $blessed_version\n" : "not found\n";
 426   return $blessed_one;
 427 }