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Build.PL
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Build.PL
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#!/usr/bin/perl
use strict;
use warnings;
use Module::Build;
my $class = Module::Build->subclass
(
class => 'Module::Build::Custom',
code => q{
sub ACTION_build {
my $self = shift;
$self->SUPER::ACTION_build;
$self->dispatch('installdeps');
}
sub ACTION_install {
my $self = shift;
print "\n\nGAL does not do a system wide install\n\n";
print "To make the libraries and scripts accessible\n";
print "modify the paths to fit your system and run the following:\n\n";
print "export PERL5LIB=\$PERL5LIB:/path/to/GAL/lib\n";
print "export PATH=\$PATH:/path/to/GAL/bin\n\n";
print "Add those lines to ~/.bash_profile or /etc/profile to\n";
print "make those changes permanent.\n\n";
print "If you want a system wide install, edit the Build.PL script and\n";
print "remove the entire subroutine (ACTION_install) where this message\n";
print "is printed run Build realclean and re-install.\n\n";
}
},
);
my $builder = $class->new(
# General
module_name => 'GAL',
dist_author => 'Barry Moore <barry.moore@genetics.utah.edu',
dist_version_from => 'lib/GAL/Annotation.pm',
license => 'Perl_5',
create_license => 1,
create_readme => 1,
# Prerequisites
requires => {
'perl' => '5.6.1',
'Bio::DB::Fasta' => 0,
'Carp' => 0,
'Config::Std' => 0,
'Cwd' => 0,
'DBI' => 0,
'DBIx::Class' => 0,
'Getopt::Long' => 0,
'IO::All' => 0,
'List::MoreUtils' => 0,
'List::Util' => 0,
'Module::Build' => 0,
'Number::Format' => 0,
'Set::IntSpan::Fast' => 0,
'Statistics::Descriptive' => 0,
'Statistics::Descriptive::Discrete' => 0,
'Text::Graph' => 0,
'Text::Table' => 0,
'Text::Graph::DataSet' => 0,
'URI::Escape' => 0,
'Text::RecordParser' => 0,
'Template' => 0,
'Config::Std' => 0,
},
build_requires => {
'TAP::Harness' => 0,
'Test::More' => 0,
'Exception::Class' => 0,
'Test::Warn' => 0,
'Test::Deep' => 0,
},
recommends => {
'Time::HiRes' => 0,
'DBIx::Class::ResultClass::HashRefInflator' => 0,
},
# Testing
use_tap_harness => 1,
tap_harness_args => {verbosity => -1,
timer => 1,
show_count => 1,
merge => 1},
test_files => [qw(
lib/GAL/t/001_annotation.t
lib/GAL/t/001_base.t
lib/GAL/t/001_pod_coverage.t
lib/GAL/t/001_test_template.t
lib/GAL/t/200_parser.t
lib/GAL/t/200_parser_basic_snp.t
lib/GAL/t/200_parser_bed.t
lib/GAL/t/200_parser_complete_genomics.t
lib/GAL/t/200_parser_complete_genomics_new.t
lib/GAL/t/200_parser_cosmic.t
lib/GAL/t/200_parser_cuffdiff_gene_exp.t
lib/GAL/t/200_parser_dbsnp_flat.t
lib/GAL/t/200_parser_gff3.t
lib/GAL/t/200_parser_hapmap_genotypes.t
lib/GAL/t/200_parser_korean_indel.t
lib/GAL/t/200_parser_korean_snp.t
lib/GAL/t/200_parser_macs_summits.t
lib/GAL/t/200_parser_maq_cns2snp.t
lib/GAL/t/200_parser_na18507_sanger_indel.t
lib/GAL/t/200_parser_quake_snp.t
lib/GAL/t/200_parser_samtools_pileup.t
lib/GAL/t/200_parser_soap_snp.t
lib/GAL/t/200_parser_solid_snp.t
lib/GAL/t/200_parser_template.t
lib/GAL/t/200_parser_template_sequence_alteration.t
lib/GAL/t/200_parser_trait_o_matic.t
lib/GAL/t/200_parser_vcfv4_0.t
lib/GAL/t/200_parser_vcfv4_1.t
lib/GAL/t/200_parser_venter_indel.t
lib/GAL/t/200_parser_venter_snp.t
lib/GAL/t/200_parser_watson_cshl.t
lib/GAL/t/300_reader.t
lib/GAL/t/300_reader_delimitedline.t
lib/GAL/t/300_reader_recordparser.t
lib/GAL/t/300_reader_template.t
lib/GAL/t/400_storage.t
lib/GAL/t/400_storage_mysql.t
lib/GAL/t/400_storage_sqlite.t
lib/GAL/t/500_schema.t
lib/GAL/t/500_schema_result_attribute.t
lib/GAL/t/500_schema_result_feature.t
lib/GAL/t/500_schema_result_feature_cds.t
lib/GAL/t/500_schema_result_feature_exon.t
lib/GAL/t/500_schema_result_feature_five_prime_utr.t
lib/GAL/t/500_schema_result_feature_gene.t
lib/GAL/t/500_schema_result_feature_intron.t
lib/GAL/t/500_schema_result_feature_mrna.t
lib/GAL/t/500_schema_result_feature_mrna_BIG.t
lib/GAL/t/500_schema_result_feature_protein.t
lib/GAL/t/500_schema_result_feature_sequence_alteration.t
lib/GAL/t/500_schema_result_feature_sequence_feature.t
lib/GAL/t/500_schema_result_feature_template.t
lib/GAL/t/500_schema_result_feature_three_prime_utr.t
lib/GAL/t/500_schema_result_feature_transcript.t
lib/GAL/t/500_schema_result_realtionship.t
lib/GAL/t/600_list.t
lib/GAL/t/600_list_categorical.t
lib/GAL/t/600_list_numeric.t
lib/GAL/t/700_writer.t
lib/GAL/t/700_writer_gff3.t
bin/t/add_reference_seq.t
bin/t/annotation_summary.t
bin/t/build_genes.t
bin/t/fastq_tool.t
bin/t/feature2gff.t
bin/t/gal_add_introns.t
bin/t/gal_coding_gene_count.t
bin/t/gal_dump_CDS_sequence.t
bin/t/gal_example_parser.t
bin/t/gal_example_seq_features.t
bin/t/gal_feature_overlaps.t
bin/t/gal_remove_transcripts.t
bin/t/gal_protein_genes.t
bin/t/gal_protein_sequence.t
bin/t/gal_CDS_sequence.t
bin/t/gal_splice_complexity.t
bin/t/gal_start_stop.t
bin/t/gal_validate_proteins.t
bin/t/gff3_validator.t
bin/t/gff_tool.t
bin/t/gtf2gff3.t
bin/t/gvf_validator.t
bin/t/map_seqids.t
bin/t/merge_data.t
bin/t/sam_inspector.t
bin/t/script_test_template.t
bin/t/ucsc2gff.t
bin/t/gal_variant_classifier.t
)],
);
$builder->create_build_script();