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#!/usr/bin/perl -w
# This is a Module::Build script for bioperl-db installation.
# See
# Uses a custom subclass of Module::Build called Bio::Root::Build
use strict;
use Bio::Root::Build;
# Set up the Bio::Root::Build object
my $build = Bio::Root::Build->new(
module_name => 'Bio',
dist_name => 'BioPerl-db',
dist_version => '1.005009_001',
dist_author => 'BioPerl Team <>',
dist_abstract => 'BioPerl-db - package for biological databases',
license => 'perl',
requires => {
'perl' => '5.6.1',
'Bio::Root::Version' => '1.006000',
'DBI' => 0
dynamic_config => 1,
create_makefile_pl => 'passthrough'
#pm_files => {} # modules in Bio are treated as if they were in lib and auto-installed
#script_files => [] # scripts in scripts directory are installed on-demand
# Ask questions
# Add extra things to MANIFEST.SKIP
# Create the build script and exit
# setup t/DBHarness.biosql.conf
sub biosql_conf {
$build->y_n("Have you already installed BioSQL? y/n", 'n') || die "\nBioSQL must be installed prior to installation of bioperl-db; see the INSTALL file\n";
my $config_file = File::Spec->catfile('t', 'DBHarness.biosql.conf');
if (-e $config_file) {
$build->y_n("Do you want to use the existing '$config_file' config file? y/n", 'y') && return;
open(my $out, ">", $config_file) or die "Error: could not write to config file '$config_file'\n";
my %config = (driver => 'mysql',
host => '',
user => 'root',
port => 3306,
password => '',
dbname => 'bioseqdb',
database => 'biosql',
schema_sql => '../biosql-schema/sql/biosqldb-mysql.sql');
$config{driver} = $build->prompt("DBD driver to use (mandatory)?", $config{driver});
$config{host} = $build->prompt("Machine to connect to (mandatory)?", $config{host});
$config{user} = $build->prompt("User to connect to server as (mandatory)?", $config{user});
$config{port} = $build->prompt("Port the server is running on (optional, '' for none)?", $config{port});
$config{port} = '' if $config{port} eq "''";
$config{password} = $build->prompt("Password (optional)?", $config{password} || 'undef');
$config{password} = '' if $config{password} eq 'undef';
# The next answer will be used to identify the database name in
# the connect string, e.g., using database=, dbname=, or sid=,
# depending on the driver.
# If this is not set the test scripts will build a temporary
# database from scratch at the beginning and destroy it at the
# end. Conversely, if you do set it then the database must exist,
# or else the tests will fail.
# Generally, it is preferred to pre-build the database, simply for
# efficiency reasons, and it will also enable debugging your
# schema content if some test acts up.
$config{dbname} = $build->prompt("Name of your existing Biosql database, as it is known to your RDBMS (optional, '' for none)?", $config{dbname});
$config{dbname} = '' if $config{dbname} eq "''";
unless ($config{dbname}) {
$config{schema_sql} = $build->prompt("Set schema_sql to use the version appropriate for your RDBMS (mandatory)", $config{schema_sql});
$config{schema_sql} = "['$config{schema_sql}']"; # don't know why it is stored as an array ref, is this correct?
# The next answer does not refer to the schema or RDBMS; it only
# identifies which of the databases supported in bioperl-db you
# want to be using. Since at present bioperl-db only supports biosql,
# this must be biosql.
$config{database} = $build->prompt("The name of the database within bioperl-db?", $config{database});
print $out "{\n";
while (my ($key, $val) = each %config) {
$val = "'$val'" unless $key eq 'schema_sql';
print $out "\t'$key' => $val,\n";
print $out "}\n";
# we deliberately don't add the config file to cleanup, but it shouldn't
# cause problems because it is in MANIFEST.SKIP
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