Merge branch 'gaas2'

.travis.yml

@@ -0,0 +1,18 @@
+language: perl
+perl:
+  - "5.30"
+  - "5.28"
+  - "5.26"
+
+before_install:
+  - git clone git://github.com/travis-perl/helpers ~/travis-perl-helpers
+  - source ~/travis-perl-helpers/init --auto
+  - sudo apt-get -y install libdb-dev
+  - sudo apt-get -y install r-base
+  - cpanm --notest Devel::Cover::Report::Coveralls
+
+script:
+  - perl Makefile.PL && make test TEST_VERBOSE=1
+
+after_success:
+  - cover -test -report coveralls

MANIFEST.SKIP

@@ -0,0 +1,49 @@
+# Avoid version control files
+\B.git\b
+\B.gitignore$
+\bRCS\b
+\bCVS\b
+,v$
+\B.svn\b
+\B.cvsignore$
+
+# Avoid Module::Build generated and utility files
+\bBuild$
+\bBuild.bat$
+\b_build
+
+# Avoid Makemaker generated and utility files
+\bMakefile$
+\bblib
+\bMakeMaker - \d
+\bpm_to_blib$
+\bblibdirs$
+^MANIFEST\.SKIP$
+
+# Avoid Devel::Cover generated files
+\bcover_db
+
+# Avoid temp and backup files
+~$
+\.tmp$
+\.old$
+\.bak$
+\#$
+\.#
+\.rej$
+\.index$
+
+# Avoid OS-specific files/dirs
+#      Mac OSX metadata
+\B.DS_Store
+#      Mac OSX SMB mount metadata files
+\B\._
+
+# Avoid archives of this distribution
+\bGAAS-v[\d\.\_]+
+^MYMETA.yml
+^MYMETA.json
+
+# other
+\B.travis.yml$
+^tmp

Makefile.PL

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+use 5.006;
+use strict;
+use warnings FATAL => 'all';
+use ExtUtils::MakeMaker;
+use File::ShareDir::Install;
+
+install_share dist => 'share';
+
+# ------------------- CREATE LIST OF EXE FILE ----------------------------------
+
+# define function to retrieve list of exe files
+sub get_list_exe{
+  my @list_exe;
+
+  opendir (DIR, "bin") or die $!;
+  while (my $file = readdir(DIR)) {
+     # Use a regular expression to ignore files beginning with a period
+     next if ($file =~ m/^\./);
+
+     #add exe file
+     push @list_exe, "bin/".$file;
+  }
+  closedir(DIR);
+
+  return \@list_exe;
+}
+my $ref_list_exe = get_list_exe();
+
+
+# ------------------- CREATE PREREQ_PM Hash -----------------------------------
+# As it is used twice, I factorze it here, to avoid de-synchronization
+
+my %prereq_hash = ( "Bio::DB::Fasta" => 0,
+                    "Bio::DB::Taxonomy" => 0,
+		    "Bio::DB::EUtilities" => 0,
+		    "Bio::FeatureIO" => 0,
+                    "Bio::Seq" => 0,
+                    "Bio::SeqIO" => 0,
+                    "Bio::Tools::CodonTable" => 0,
+                    "Bio::Tools::GFF" => 0,
+                    "Carp" => 0,
+                    "Clone" => 0,
+                    "Cwd" => 0,
+                    "Exporter" => 0,
+                    "File::Basename" => 0,
+                    "File::Copy" => 0,
+                    "File::Share" => 0,
+                    "Getopt::Long" => 0,
+                    "IO::File" => 0,
+                    "IPC::Open2" => 0,
+                    "IPC::Cmd" => 0,
+                    "JSON" => 0,
+                    "LWP::UserAgent" => 0,
+                    "List::MoreUtils" => 0,
+                    "POSIX" => 0,
+                    "Pod::Usage" => 0,
+                    "Scalar::Util" => 0,
+                    "Sort::Naturally" => 0,
+                    "Statistics::R" => 0,
+                    "Time::Piece" => 0,
+                    "Time::Seconds" => 0,
+                    "Try::Tiny" => 0,
+                    "URI::Escape" => 0,
+                    "strict" => 0,
+                    "warnings" => 0
+                  );
+
+# ------------------- CREATE the WriteMakefile hash ----------------------------
+# will be used to create the WriteMakefile object
+
+my %WriteMakefileArgs = (
+  NAME            => 'GAAS',
+  AUTHOR          => 'Jacques Dainat <[email protected]>',
+  VERSION_FROM    => 'lib/GAAS/GAAS.pm',
+  ABSTRACT        => 'Genome Assembly and Annotation Service toolkit at NBISweden',
+  LICENSE         => 'gpl_3',
+  PREREQ_PM       => \%prereq_hash, # give a ref to the hash
+  MIN_PERL_VERSION => '5.006',
+  BUILD_REQUIRES  => {"ExtUtils::MakeMaker" => 6.31,
+                      "File::ShareDir::Install" => 0
+                    },
+  TEST_REQUIRES   => {"Test::More" => 0
+                     },
+  EXE_FILES       => $ref_list_exe,
+  META_MERGE      => {
+      'meta-spec' => { version => 2 },
+      resources   => {
+          repository => {
+              type => 'git',
+              url  => 'https://github.com/NBISweden/GAAS.git',
+              web  => 'https://github.com/NBISweden/GAAS',
+          },
+          bugtracker => {web => 'https://github.com/NBISweden/GAAS/issues'},
+          homepage   => 'https://nbis.se',
+      },
+  },
+  dist  => { COMPRESS => 'gzip -9f', SUFFIX => 'gz', },
+  clean => { FILES => 'GAAS-*' },
+);
+
+my %FallbackPrereqs = %prereq_hash;
+
+
+unless ( eval { ExtUtils::MakeMaker->VERSION(6.63_03) } ) {
+  delete $WriteMakefileArgs{TEST_REQUIRES};
+  delete $WriteMakefileArgs{BUILD_REQUIRES};
+  $WriteMakefileArgs{PREREQ_PM} = \%FallbackPrereqs;
+}
+
+delete $WriteMakefileArgs{CONFIGURE_REQUIRES}
+  unless eval { ExtUtils::MakeMaker->VERSION(6.52) };
+
+if ( $^O eq 'MSWin32' ) {
+	$WriteMakefileArgs{PREREQ_PM}{'Win32'} = $FallbackPrereqs{'Win32'} = '0';
+}
+
+WriteMakefile(%WriteMakefileArgs);
+
+#Mandatory otherwise the data files from the share folder will not be copied.
+package MY;
+use File::ShareDir::Install 'postamble';