scripts/bioperl_application_installer.PLS

   1 #!/usr/local/bin/perl
   2 # BioPerl script for Bio::Installer
   3 #
   4 # Cared for by Albert Vilella <avilella@ebi.ac.uk, avilella@ub.edu>
   5 #
   6 #       based on the CPAN::FirstTime module
   7 #
   8 # Copyright Albert Vilella
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 bioperl_application_installer - downloads and installs runnables
  17
  18 =head1 SYNOPSIS
  19
  20 bioperl_application_installer
  21
  22 =head1 DESCRIPTION
  23
  24 This script will ask the user which programs wants to install and
  25 where. It will download the packages, decompress them (if necessary)
  26 and compile/install them in the specified directory.
  27
  28 =head1 AUTHOR
  29
  30 Albert Vilella, avilella-AT-ebi-DOT-ac-DOT-uk,avilella-AT-ub-DOT-edu
  31
  32 =head1 TODO
  33
  34 Check if the programs are already installed in the computer and prompt
  35 it so that the user is at least aware of it.
  36
  37 Check for the available installers, instead of hard-coding
  38 $INSTALLERLIST in this script.
  39
  40 =cut
  41
  42 use strict;
  43 use ExtUtils::MakeMaker;
  44 use Data::Dumper;
  45 use Bio::Factory::ObjectFactory;
  46
  47 use vars qw($DEFAULT $CONFIG $INSTALLERLIST);
  48
  49 BEGIN {
  50     $DEFAULT = 'bioperl-runnables';
  51     $INSTALLERLIST = [
  52                       'Clustalw',
  53                       'EMBOSS',
  54                       'TCoffee',
  55                       'PAML',
  56                      ];
  57 }
  58
  59 my $dir = shift @ARGV || $DEFAULT;
  60 init($dir);
  61
  62 1;
  63
  64
  65 ################################################################################
  66
  67 sub init {
  68     my($configpm) = @_;
  69     use Config;
  70     local($/) = "\n";
  71     local($\) = "";
  72     local($|) = 1;
  73
  74     my($ans,$default);
  75
  76     #
  77     # Files, directories
  78     #
  79
  80     print qq[
  81
  82 This script will install the runnable programs associated with
  83 bioperl-run.
  84
  85 Bioperl-run contain modules that provides a PERL interface to various
  86 bioinformatics applications. This allows various applications to be
  87 used with common bioperl objects.
  88
  89 If you do not want to enter a dialog now, you can answer 'no' to this
  90 question.
  91
  92 ];
  93
  94     my $manual_conf =
  95         ExtUtils::MakeMaker::prompt("Are you ready for manual configuration?",
  96                                     "yes");
  97     my $fastread;
  98     {
  99         local $^W;
 100         if ($manual_conf =~ /^\s*y/i) {
 101             $fastread = 0;
 102             *prompt = \&ExtUtils::MakeMaker::prompt;
 103         } else {
 104             print "Done.\n\n";
 105             exit;
 106         }
 107     }
 108     print qq{
 109
 110 The following questions are intended to help you with the
 111 installation.
 112
 113 };
 114
 115     $default = File::Spec->catdir( $ENV{'HOME'}, $configpm);
 116     while ($ans = prompt("Where do you want to install the runnables in your computer?",$default)) {
 117         unless (File::Spec->file_name_is_absolute($ans)) {
 118             require Cwd;
 119             my $cwd = Cwd::cwd();
 120             my $absans = File::Spec->catdir($cwd,$ans);
 121             warn "The path '$ans' is not an absolute path. Please specify an absolute path\n";
 122             $default = $absans;
 123             next;
 124         }
 125         eval { File::Path::mkpath($ans); }; # dies if it can't
 126         if ($@) {
 127             warn "Couldn't create directory $ans.
 128 Please retry.\n";
 129             next;
 130         }
 131         if (-d $ans && -w _) {
 132             print qq{
 133 Directory $ans successfully created.
 134
 135 };
 136
 137             last;
 138         } else {
 139             warn "Couldn't find directory $ans
 140   or directory is not writable. Please retry.\n";
 141         }
 142     }
 143
 144     print qq{
 145
 146 The script will need a few external programs to work properly.
 147 Please correct me, if I guess the wrong path for a program. Don\'t
 148 panic if you do not have some of them, just press ENTER for those.
 149
 150 };
 151
 152     my $old_warn = $^W;
 153     local $^W if $^O eq 'MacOS';
 154     my(@path) = split /$Config{'path_sep'}/, $ENV{'PATH'};
 155     local $^W = $old_warn;
 156     my $progname;
 157     for $progname (qw/gzip tar unzip make links wget ncftpget ncftp ftp gpg/) {
 158         if ($^O eq 'MacOS') {
 159             $CONFIG->{$progname} = 'not_here';
 160             next;
 161         }
 162         my $progcall = $progname;
 163         # we don't need ncftp if we have ncftpget
 164         next if $progname eq "ncftp" && $CONFIG->{ncftpget} gt " ";
 165         my $path = $CONFIG->{$progname}
 166             || $Config::Config{$progname}
 167                 || "";
 168         if (File::Spec->file_name_is_absolute($path)) {
 169             # testing existence is not good enough, some have these exe
 170             # extensions
 171
 172             # warn "Warning: configured $path does not exist\n" unless -e $path;
 173             # $path = "";
 174         } else {
 175             $path = '';
 176         }
 177         unless ($path) {
 178             # e.g. make -> nmake
 179             $progcall = $Config::Config{$progname} if $Config::Config{$progname};
 180         }
 181
 182         $path ||= find_exe($progcall,[@path]);
 183         warn "Warning: $progcall not found in PATH\n" unless
 184             $path; # not -e $path, because find_exe already checked that
 185         $ans = prompt("Where is your $progname program?",$path) || $path;
 186         $CONFIG->{$progname} = $ans;
 187     }
 188     my $path = $CONFIG->{'pager'} ||
 189         $ENV{PAGER} || find_exe("less",[@path]) ||
 190             find_exe("more",[@path]) || ($^O eq 'MacOS' ? $ENV{EDITOR} : 0 )
 191                 || "more";
 192     $ans = prompt("What is your favorite pager program?",$path);
 193     $CONFIG->{'pager'} = $ans;
 194     $path = $CONFIG->{'shell'};
 195     if (File::Spec->file_name_is_absolute($path)) {
 196         warn "Warning: configured $path does not exist\n" unless -e $path;
 197         $path = "";
 198     }
 199     $path ||= $ENV{SHELL};
 200     if ($^O eq 'MacOS') {
 201         $CONFIG->{'shell'} = 'not_here';
 202     } else {
 203         $path =~ s,\\,/,g if $^O eq 'os2'; # Cosmetic only
 204         $ans = prompt("What is your favorite shell?",$path);
 205         $CONFIG->{'shell'} = $ans;
 206     }
 207
 208     print qq{
 209
 210 Which programs would you like to install?
 211
 212 };
 213     my @selected_programs;
 214     my $prompt = "Select the programs you would like to install (by number),
 215 put them on one line, separated by blanks, e.g. '1 2 4'";
 216
 217     push (@selected_programs, @$INSTALLERLIST);
 218     @selected_programs = picklist (\@selected_programs, $prompt);
 219     push @{$CONFIG->{selected_programs_list}}, @selected_programs;
 220
 221     print qq{
 222
 223 The selected programs will now be installed
 224
 225 };
 226
 227 # TODO: Check for the available installers, instead of hard-coding
 228 # $INSTALLERLIST in this script.
 229 #     my @l;
 230 #     for my $i (@INC) {
 231 #         next unless (-e $i."/My/Stuff/");
 232 #         opendir(X,$i."/My/Stuff")|| warn "$!";
 233 #         push @l,readdir(X);
 234 #     }
 235
 236 #     find sub { push(@l, $File::Find::name) if -f && /\.pm$/ },
 237 #         map { "$_/My/Module" } @INC;
 238
 239     foreach my $program (@selected_programs) {
 240         my $type = 'Bio::Installer::' . $program;
 241         my $factory = new Bio::Factory::ObjectFactory(-type => $type);
 242         my $instance = $factory->create_object();
 243         $instance->destination_install_dir($default);
 244         $instance->download();
 245         $instance->install();
 246     }
 247
 248
 249 }
 250
 251 sub picklist {
 252     my($items,$prompt,$default,$require_nonempty,$empty_warning)=@_;
 253     $default ||= '';
 254
 255     my $pos = 0;
 256
 257     my @nums;
 258     while (1) {
 259
 260         # display, at most, 15 items at a time
 261         my $limit = $#{ $items } - $pos;
 262         $limit = 15 if $limit > 15;
 263
 264         # show the next $limit items, get the new position
 265         $pos = display_some($items, $limit, $pos);
 266         $pos = 0 if $pos >= @$items;
 267
 268         my $num = prompt($prompt,$default);
 269
 270         @nums = split (' ', $num);
 271         my $i = scalar @$items;
 272         (warn "invalid items entered, try again\n"), next
 273             if grep (/\D/ || $_ < 1 || $_ > $i, @nums);
 274         if ($require_nonempty) {
 275             (warn "$empty_warning\n");
 276         }
 277         print "\n";
 278
 279         # a blank line continues...
 280         next unless @nums;
 281         last;
 282     }
 283     for (@nums) { $_-- }
 284     @{$items}[@nums];
 285 }
 286
 287
 288 sub display_some {
 289         my ($items, $limit, $pos) = @_;
 290         $pos ||= 0;
 291
 292         my @displayable = @$items[$pos .. ($pos + $limit)];
 293     for my $item (@displayable) {
 294                 printf "(%d) %s\n", ++$pos, $item;
 295     }
 296         printf("%d more items, hit SPACE RETURN to show them\n",
 297                (@$items - $pos)
 298               )
 299             if $pos < @$items;
 300         return $pos;
 301 }
 302
 303
 304 sub find_exe {
 305     my($exe,$path) = @_;
 306     my($dir);
 307     #warn "in find_exe exe[$exe] path[@$path]";
 308     for $dir (@$path) {
 309         my $abs = File::Spec->catfile($dir,$exe);
 310         if (($abs = MM->maybe_command($abs))) {
 311             return $abs;
 312         }
 313     }
 314 }
 315