1 ## --Makefile.PL for Bioperl-pipeline distribution--##
2 ## ----------------------------------------------------##
4 ##----------------------------------------------------
7 # Basically this is a standard Makefile with a hash of
8 # needed packages which are tested at the start
10 # If you want help with this Makefile get in touch with
11 # the developers by sending a message to bioperl-l@bioperl.org.
13 use ExtUtils::MakeMaker;
17 # All Bioperl dependencies on external modules are defined here
19 'IO::String' => '0.0/IO handle to read or write to a string/GenBank+GenPept sequence retrieval, Variation code/Bio::DB::*,Bio::Variation::*,Bio::Tools::Blast::Run::Webblast, Bio::Index::Blast',
20 'File::Temp' => '0.0/Temporary File creation/Bio::Root::IO uses if present/Bio::DB::WebDBSeqI, Bio::Seq::LargePrimarySeq',
21 'XML::Parser::PerlSAX' => '0.0/XML SAX parser/Pise Applications/Pise::Job',
22 'HTML::Parser' => '0.0/HTML Parser/Pise Applications/Pise::Job');
26 my ($ver,$desc,$expl,$module) = split( /\// , $str);
27 if( !eval "require($name)") {
28 print "External Module $name, $desc,\n is not installed on this computer.\n The $module in bioperl-run needs it for $expl\n\n";
36 # Generate sub testing package system
40 # make mini test targets for playing around with
43 opendir(DIR,"t") || warn "No test directory. Weird!";
44 @files = readdir(DIR);
47 foreach my $file (@files) {
48 $file =~ /(\w+)\.t/ || next;
50 $line = "test_$file :: pure_all\n\tPERL_DL_NONLAZY=1 \$(FULLPERL) -I\$(INST_ARCHLIB) -I\$(INST_LIB) -I\$(PERL_ARCHLIB) -I\$(PERL_LIB) -e \'use Test::Harness qw(&runtests \$\$verbose); \$\$verbose=\$(TEST_VERBOSE); runtests \@ARGV;\' t/$file.t\n";
53 $tset .= "$file \\\n";
56 $tline = join('',@tline);
57 $tline = "show_tests :\n\t\@echo \'type make test_<subtest> to run\'\n\t\@echo '$tset'\n$tline\n";
59 print STDERR "Generated sub tests. go make show_tests to see available subtests\n";
66 # Talk to Elia Stupka (<elia@fugu-sg.org>) or bioperl-l@bioperl.org for more info.
69 # Let the code begin...
72 my $DISTNAME = "bioperl-run";
75 my $proceed = prompt("Do you want to run the Pise tests (requires a network connection) y/n",'n');
76 if( $proceed =~ /^[yY]/) {
77 my $address = prompt("Enter your email address (no default)",'');
79 if (open T,">t/pise-email.test") {
82 } else { warn("Cannot open file t/pise-email.test for writing - no Pise tests will be run"); }
84 if( -e "t/pise-email.test" ) {
85 unlink "t/pise-email.test";
88 #$do_autoload_finesse = 0;
95 foreach $name ( keys %packages ) {
96 if( &check_package($name,$packages{$name}) == 1 ) {
106 There are some external packages and perl modules, listed above, which
107 bioperl-run uses. This only effects the functionality which is listed above:
108 the rest of bioperl will work fine.
110 The installation of these external packages is very simple. You
111 can read more about bioperl external dependencies at
113 http://bioperl.org/Core/external.shtml
115 Enjoy the rest of bioperl, which you can use after going 'make install'
122 DISTNAME => $DISTNAME,
124 'dist' => { COMPRESS => 'gzip -9f',
126 DIST_DEFAULT => 'all tardist',
129 'AUTHOR' => 'FuguI Team (fugui@fugu-sg.org)',
130 'ABSTRACT' => 'Generic Feature Database',
132 'realclean' => { FILES => join(' ',@BACKUP_FILES) }