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## --Makefile.PL for Bioperl core module distribution--##
## ----------------------------------------------------##
## $Id: Makefile.PL,v 1.30.2.5 2002/03/17 00:00:47 jason Exp $
##----------------------------------------------------
#
# Basically this is a standard Makefile with a hash of
# needed packages which are tested at the start
#
# If you want help with this Makefile get in touch with
# the developers by sending a message to bioperl-l@bioperl.org.
# All Bioperl dependencies on external modules are defined here
%packages = (
'HTTP::Request::Common' => '0.0/Part of the LWP package/GenBank+GenPept sequence retrieval, remote http Blast jobs/Bio::DB::*,Bio::Tools::Run::RemoteBlast',
'LWP::UserAgent' => '0.0/Part of the LWP package/GenBank+GenPept sequence retrieval, remote http Blast jobs/Bio::DB::*,Bio::Tools::Run::RemoteBlast',
'Ace' => '0.0/Aceperl/access of ACeDB database/Bio::DB::Ace',
'IO::Scalar' => '0.0/IO handle to read or write to a scalar/remote http Blast jobs/Bio::Tools::Blast::Run::Webblast',
'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',
'XML::Parser' => '0.0/Parsing of XML documents/Bio::Variation code, GAME parser/Bio::SeqIO::game,Bio::Variation::*',
'XML::Writer' => '0.0/Parsing + writing of XML documents/Bio::Variation code, GAME parser/Bio::SeqIO::game,Bio::Variation::*',
'XML::Parser::PerlSAX' => '0.0/Parsing of XML documents/Bio::Variation code, GAME parser/Bio::SeqIO::game,Bio::Variation::*',
'XML::Twig' => '0.0/Available on CPAN/parsing of XML documents/Module Bio::Variation::IO::xml.pm',
'File::Temp' => '0.0/Temporary File creation/Bio::DB::WebDBSeqI, Bio::Seq::LargePrimarySeq',
'SOAP::Lite' => '0.0/SOAP protocol/XEMBL Services (also Bibliographic queries in Biblio::) /Bio::DB::XEMBLService',
'HTML::Parser' => '0.0/HTML parsing of GDB page/Bio::DB::GDB',
'DBD::mysql' => '0.0/Mysql driver/loading and querying of Mysql-based GFF feature databases/Bio::DB::GFF',
'GD' => '1.3/Graphical Drawing Toolkit/Rendering Sequences and Features/Bio::Graphics',
'Storable' => '0.0/Persistent object storage and retrieval/Storing sequence objects in local file cache/Bio::DB::FileCache',
# rare function let's not scare people
# 'srsperl.pm' => '0.0/Sequence Retrieval System (SRS) perl API/alternative way of retrieving sequences/Bio::LiveSeq::IO::SRS.pm'
);
sub check_package {
my ($name,$str) = @_;
my ($ver,$desc,$expl,$module) = split( /\// , $str);
if( !eval "require($name)") {
print "External Module $name, $desc,\n is not installed on this computer.\n The $module in Bioperl needs it for $expl\n\n";
return 1;
}
return 0;
}
#
# Generate sub testing package system
#
#
# make mini test targets for playing around with
# in testing...
opendir(DIR,"t") || warn "No test directory. Weird!";
@files = readdir(DIR);
shift @files;
shift @files;
foreach my $file (@files) {
$file =~ /(\w+)\.t/ || next;
$file = $1;
$line = "test_$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/$file.t\n";
push(@tline,$line);
push(@targets,$file);
$tset .= "$file \\\n";
}
$tline = join('',@tline);
$tline = "show_tests :\n\t\@echo \'type make test_<subtest> to run\'\n\t\@echo '$tset'\n$tline\n";
print STDERR "Generated sub tests. go make show_tests to see available subtests\n";
sub MY::postamble {
$tline;
}
#
# Prompt user for BioGFFDB stuff
#
if( eval { require DBI } ) {
my $proceed = user_prompt("Do you want to run the BioGFFDB tests (requires mysql) y/n",'n');
if( $proceed eq 'y' ) {
system("touch t/do_biodbgff.tests");
} else {
if( -e "t/do_biodbgff.tests" ) {
unlink "t/do_biodbgff.tests";
}
}
}
sub user_prompt ($;$) {
my($mess,$def)=@_;
Carp::confess("prompt function called without an argument") unless defined $mess;
my $dispdef = defined $def ? "[$def] " : " ";
$def = defined $def ? $def : "";
my $ans;
local $|=1;
print STDERR "$mess $dispdef";
chomp($ans = <STDIN>);
return ($ans ne '') ? $ans : $def;
}
#
# Talk to Ewan (<birney@ebi.ac.uk>) or bioperl-l@bioperl.org for more info.
#
# Let the code begin...
require 5.005;
use ExtUtils::MakeMaker;
$do_autoload_finesse = 0;
$NAME = 'Bio';
$DISTNAME = "bioperl";
$VERSION = "1.00";
if( $do_autoload_finesse == 1 ) {
fatal("Autoload finessing does not work at the moment!");
}
@BACKUP_FILES = qw(./Seq.pm.bak);
#
# This does an inplace edit on Seq.pm
#
if( $do_autoload_finesse ) {
print "Bioperl module installation\nPreparing modules for AUTOLOADing...";
`perl -p -i.bak -e 's/#__END__/__END__/' Seq.pm`;
print "done.\n\n";
}
$error = 0;
print "\n";
foreach $name ( keys %packages ) {
if( &check_package($name,$packages{$name}) == 1 ) {
$error = 1;
}
}
if( $error == 1 ) {
print <<QQ_ERROR_QQ;
Warning:
There are some external packages and perl modules, listed above, which
bioperl uses. This only effects the functionality which is listed above:
the rest of bioperl will work fine.
The installation of these external packages is very simple. You
can read more about bioperl external dependencies at
http://bioperl.org/Core/external.shtml
Enjoy the rest of bioperl, which you can use after going 'make install'
QQ_ERROR_QQ
}
WriteMakefile(
NAME => $NAME,
DISTNAME => $DISTNAME,
VERSION => $VERSION,
'dist' => { COMPRESS => 'gzip -9f',
SUFFIX => '.gz',
DIST_DEFAULT => 'all tardist',
},
($] ge '5.005') ? (
'AUTHOR' => 'Bioperl Team (bioperl-l@bioperl.org)',
'ABSTRACT' => 'Bioinformatics Toolkit',
) : (),
'realclean' => { FILES => join(' ',@BACKUP_FILES) }
);
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