From 71b1fe3e03bf7714329d8a58be3847a7108efdcc Mon Sep 17 00:00:00 2001 From: Robert Buels Date: Wed, 27 Jun 2012 12:55:18 -0400 Subject: [PATCH] move perl modules to lib/perl5 --- bin/bam-to-json.pl | 2 +- bin/biodb-to-json.pl | 2 +- bin/draw-basepair-track.pl | 2 +- bin/flatfile-to-json.pl | 2 +- bin/generate-names.pl | 2 +- bin/prepare-refseqs.pl | 2 +- bin/remove-track.pl | 2 +- bin/ucsc-to-json.pl | 2 +- bin/wig-to-json.pl | 2 +- lib/{ => perl5}/ArrayRepr.pm | 0 lib/{ => perl5}/Bio/FeatureIO/bed.pm | 0 lib/{ => perl5}/Bio/JBrowse/Cmd.pm | 0 lib/{ => perl5}/Bio/JBrowse/Cmd/BioDBToJson.pm | 0 lib/{ => perl5}/Bio/JBrowse/Cmd/FlatFileToJson.pm | 0 lib/{ => perl5}/Bio/JBrowse/Cmd/NCFormatter.pm | 0 lib/{ => perl5}/Bio/JBrowse/Cmd/RemoveTrack.pm | 0 lib/{ => perl5}/Bio/JBrowse/FeatureStream.pm | 0 lib/{ => perl5}/Bio/JBrowse/FeatureStream/BioPerl.pm | 0 lib/{ => perl5}/Bio/JBrowse/FeatureStream/GFF3_LowLevel.pm | 0 lib/{ => perl5}/ExternalSorter.pm | 0 lib/{ => perl5}/FastaDatabase.pm | 0 lib/{ => perl5}/FeatureTrack.pm | 0 lib/{ => perl5}/GenomeDB.pm | 0 lib/{ => perl5}/ImageTrack.pm | 0 lib/{ => perl5}/ImageTrackRenderer.pm | 0 lib/{ => perl5}/IntervalStore.pm | 0 lib/{ => perl5}/JBlibs.pm | 0 lib/{ => perl5}/JsonFileStorage.pm | 0 lib/{ => perl5}/JsonGenerator.pm | 0 lib/{ => perl5}/LazyNCList.pm | 0 lib/{ => perl5}/LazyPatricia.pm | 0 lib/{ => perl5}/NCLSorter.pm | 0 lib/{ => perl5}/NCList.pm | 0 lib/{ => perl5}/NameHandler.pm | 0 lib/{ => perl5}/TiledImage.pm | 0 lib/{ => perl5}/TiledImage/DBPrimStorage.pm | 0 lib/{ => perl5}/TiledImage/MemoryPrimStorage.pm | 0 lib/{ => perl5}/TiledImage/demo-tiledimage.pl | 0 lib/{ => perl5}/TiledImage/gdtile.sql | 0 lib/{ => perl5}/TrackImage.pm | 0 40 files changed, 9 insertions(+), 9 deletions(-) rename lib/{ => perl5}/ArrayRepr.pm (100%) rename lib/{ => perl5}/Bio/FeatureIO/bed.pm (100%) rename lib/{ => perl5}/Bio/JBrowse/Cmd.pm (100%) rename lib/{ => perl5}/Bio/JBrowse/Cmd/BioDBToJson.pm (100%) rename lib/{ => perl5}/Bio/JBrowse/Cmd/FlatFileToJson.pm (100%) rename lib/{ => perl5}/Bio/JBrowse/Cmd/NCFormatter.pm (100%) rename lib/{ => perl5}/Bio/JBrowse/Cmd/RemoveTrack.pm (100%) rename lib/{ => perl5}/Bio/JBrowse/FeatureStream.pm (100%) rename lib/{ => perl5}/Bio/JBrowse/FeatureStream/BioPerl.pm (100%) rename lib/{ => perl5}/Bio/JBrowse/FeatureStream/GFF3_LowLevel.pm (100%) rename lib/{ => perl5}/ExternalSorter.pm (100%) rename lib/{ => perl5}/FastaDatabase.pm (100%) rename lib/{ => perl5}/FeatureTrack.pm (100%) rename lib/{ => perl5}/GenomeDB.pm (100%) rename lib/{ => perl5}/ImageTrack.pm (100%) rename lib/{ => perl5}/ImageTrackRenderer.pm (100%) rename lib/{ => perl5}/IntervalStore.pm (100%) rename lib/{ => perl5}/JBlibs.pm (100%) rename lib/{ => perl5}/JsonFileStorage.pm (100%) rename lib/{ => perl5}/JsonGenerator.pm (100%) rename lib/{ => perl5}/LazyNCList.pm (100%) rename lib/{ => perl5}/LazyPatricia.pm (100%) rename lib/{ => perl5}/NCLSorter.pm (100%) rename lib/{ => perl5}/NCList.pm (100%) rename lib/{ => perl5}/NameHandler.pm (100%) rename lib/{ => perl5}/TiledImage.pm (100%) rename lib/{ => perl5}/TiledImage/DBPrimStorage.pm (100%) rename lib/{ => perl5}/TiledImage/MemoryPrimStorage.pm (100%) rename lib/{ => perl5}/TiledImage/demo-tiledimage.pl (100%) rename lib/{ => perl5}/TiledImage/gdtile.sql (100%) rename lib/{ => perl5}/TrackImage.pm (100%) diff --git a/bin/bam-to-json.pl b/bin/bam-to-json.pl index 0cae45fc16..fc1a9e8734 100755 --- a/bin/bam-to-json.pl +++ b/bin/bam-to-json.pl @@ -64,7 +64,7 @@ =head1 OPTIONS use warnings; use FindBin qw($Bin); -use lib "$Bin/../lib"; +use lib "$Bin/../lib/perl5"; use JBlibs; use Pod::Usage; diff --git a/bin/biodb-to-json.pl b/bin/biodb-to-json.pl index 575bc424ab..9ae567b386 100755 --- a/bin/biodb-to-json.pl +++ b/bin/biodb-to-json.pl @@ -1,7 +1,7 @@ #!/usr/bin/env perl use strict; use FindBin qw($RealBin); -use lib "$RealBin/../lib"; +use lib "$RealBin/../lib/perl5"; use JBlibs; use Bio::JBrowse::Cmd::BioDBToJson; diff --git a/bin/draw-basepair-track.pl b/bin/draw-basepair-track.pl index 90beced3fe..eab9338661 100755 --- a/bin/draw-basepair-track.pl +++ b/bin/draw-basepair-track.pl @@ -70,7 +70,7 @@ =head1 OPTIONS use warnings; use FindBin qw($Bin); -use lib "$Bin/../lib"; +use lib "$Bin/../lib/perl5"; use JBlibs; use File::Basename; diff --git a/bin/flatfile-to-json.pl b/bin/flatfile-to-json.pl index 51ac1a84c4..30b6747500 100755 --- a/bin/flatfile-to-json.pl +++ b/bin/flatfile-to-json.pl @@ -1,7 +1,7 @@ #!/usr/bin/env perl use strict; use FindBin qw($RealBin); -use lib "$RealBin/../lib"; +use lib "$RealBin/../lib/perl5"; use JBlibs; use Bio::JBrowse::Cmd::FlatFileToJson; diff --git a/bin/generate-names.pl b/bin/generate-names.pl index dffd86ef36..b5f8c78fa9 100755 --- a/bin/generate-names.pl +++ b/bin/generate-names.pl @@ -40,7 +40,7 @@ =head1 OPTIONS use warnings; use FindBin qw($Bin); -use lib "$Bin/../lib"; +use lib "$Bin/../lib/perl5"; use JBlibs; use Fcntl ":flock"; diff --git a/bin/prepare-refseqs.pl b/bin/prepare-refseqs.pl index 9363f7fc3e..120adee67d 100755 --- a/bin/prepare-refseqs.pl +++ b/bin/prepare-refseqs.pl @@ -66,7 +66,7 @@ =head1 OPTIONS use POSIX; use Getopt::Long; -use lib "$Bin/../lib"; +use lib "$Bin/../lib/perl5"; use JBlibs; use JsonGenerator; diff --git a/bin/remove-track.pl b/bin/remove-track.pl index b2d6744016..1966d3dd6b 100755 --- a/bin/remove-track.pl +++ b/bin/remove-track.pl @@ -1,7 +1,7 @@ #!/usr/bin/env perl use FindBin '$RealBin'; -use lib "$RealBin/../lib"; +use lib "$RealBin/../lib/perl5"; use JBlibs; use Bio::JBrowse::Cmd::RemoveTrack; diff --git a/bin/ucsc-to-json.pl b/bin/ucsc-to-json.pl index 7b555e81c6..2d6ab8d0c9 100755 --- a/bin/ucsc-to-json.pl +++ b/bin/ucsc-to-json.pl @@ -93,7 +93,7 @@ =head1 EXAMPLE use warnings; use FindBin qw($Bin); -use lib "$Bin/../lib"; +use lib "$Bin/../lib/perl5"; use JBlibs; use Pod::Usage; diff --git a/bin/wig-to-json.pl b/bin/wig-to-json.pl index 703010e9af..f65c48f7ba 100755 --- a/bin/wig-to-json.pl +++ b/bin/wig-to-json.pl @@ -86,7 +86,7 @@ =head1 OPTIONS use warnings; use FindBin qw($Bin); -use lib "$Bin/../lib"; +use lib "$Bin/../lib/perl5"; use JBlibs; use File::Basename; diff --git a/lib/ArrayRepr.pm b/lib/perl5/ArrayRepr.pm similarity index 100% rename from lib/ArrayRepr.pm rename to lib/perl5/ArrayRepr.pm diff --git a/lib/Bio/FeatureIO/bed.pm b/lib/perl5/Bio/FeatureIO/bed.pm similarity index 100% rename from lib/Bio/FeatureIO/bed.pm rename to lib/perl5/Bio/FeatureIO/bed.pm diff --git a/lib/Bio/JBrowse/Cmd.pm b/lib/perl5/Bio/JBrowse/Cmd.pm similarity index 100% rename from lib/Bio/JBrowse/Cmd.pm rename to lib/perl5/Bio/JBrowse/Cmd.pm diff --git a/lib/Bio/JBrowse/Cmd/BioDBToJson.pm b/lib/perl5/Bio/JBrowse/Cmd/BioDBToJson.pm similarity index 100% rename from lib/Bio/JBrowse/Cmd/BioDBToJson.pm rename to lib/perl5/Bio/JBrowse/Cmd/BioDBToJson.pm diff --git a/lib/Bio/JBrowse/Cmd/FlatFileToJson.pm b/lib/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm similarity index 100% rename from lib/Bio/JBrowse/Cmd/FlatFileToJson.pm rename to lib/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm diff --git a/lib/Bio/JBrowse/Cmd/NCFormatter.pm b/lib/perl5/Bio/JBrowse/Cmd/NCFormatter.pm similarity index 100% rename from lib/Bio/JBrowse/Cmd/NCFormatter.pm rename to lib/perl5/Bio/JBrowse/Cmd/NCFormatter.pm diff --git a/lib/Bio/JBrowse/Cmd/RemoveTrack.pm b/lib/perl5/Bio/JBrowse/Cmd/RemoveTrack.pm similarity index 100% rename from lib/Bio/JBrowse/Cmd/RemoveTrack.pm rename to lib/perl5/Bio/JBrowse/Cmd/RemoveTrack.pm diff --git a/lib/Bio/JBrowse/FeatureStream.pm b/lib/perl5/Bio/JBrowse/FeatureStream.pm similarity index 100% rename from lib/Bio/JBrowse/FeatureStream.pm rename to lib/perl5/Bio/JBrowse/FeatureStream.pm diff --git a/lib/Bio/JBrowse/FeatureStream/BioPerl.pm b/lib/perl5/Bio/JBrowse/FeatureStream/BioPerl.pm similarity index 100% rename from lib/Bio/JBrowse/FeatureStream/BioPerl.pm rename to lib/perl5/Bio/JBrowse/FeatureStream/BioPerl.pm diff --git a/lib/Bio/JBrowse/FeatureStream/GFF3_LowLevel.pm b/lib/perl5/Bio/JBrowse/FeatureStream/GFF3_LowLevel.pm similarity index 100% rename from lib/Bio/JBrowse/FeatureStream/GFF3_LowLevel.pm rename to lib/perl5/Bio/JBrowse/FeatureStream/GFF3_LowLevel.pm diff --git a/lib/ExternalSorter.pm b/lib/perl5/ExternalSorter.pm similarity index 100% rename from lib/ExternalSorter.pm rename to lib/perl5/ExternalSorter.pm diff --git a/lib/FastaDatabase.pm b/lib/perl5/FastaDatabase.pm similarity index 100% rename from lib/FastaDatabase.pm rename to lib/perl5/FastaDatabase.pm diff --git a/lib/FeatureTrack.pm b/lib/perl5/FeatureTrack.pm similarity index 100% rename from lib/FeatureTrack.pm rename to lib/perl5/FeatureTrack.pm diff --git a/lib/GenomeDB.pm b/lib/perl5/GenomeDB.pm similarity index 100% rename from lib/GenomeDB.pm rename to lib/perl5/GenomeDB.pm diff --git a/lib/ImageTrack.pm b/lib/perl5/ImageTrack.pm similarity index 100% rename from lib/ImageTrack.pm rename to lib/perl5/ImageTrack.pm diff --git a/lib/ImageTrackRenderer.pm b/lib/perl5/ImageTrackRenderer.pm similarity index 100% rename from lib/ImageTrackRenderer.pm rename to lib/perl5/ImageTrackRenderer.pm diff --git a/lib/IntervalStore.pm b/lib/perl5/IntervalStore.pm similarity index 100% rename from lib/IntervalStore.pm rename to lib/perl5/IntervalStore.pm diff --git a/lib/JBlibs.pm b/lib/perl5/JBlibs.pm similarity index 100% rename from lib/JBlibs.pm rename to lib/perl5/JBlibs.pm diff --git a/lib/JsonFileStorage.pm b/lib/perl5/JsonFileStorage.pm similarity index 100% rename from lib/JsonFileStorage.pm rename to lib/perl5/JsonFileStorage.pm diff --git a/lib/JsonGenerator.pm b/lib/perl5/JsonGenerator.pm similarity index 100% rename from lib/JsonGenerator.pm rename to lib/perl5/JsonGenerator.pm diff --git a/lib/LazyNCList.pm b/lib/perl5/LazyNCList.pm similarity index 100% rename from lib/LazyNCList.pm rename to lib/perl5/LazyNCList.pm diff --git a/lib/LazyPatricia.pm b/lib/perl5/LazyPatricia.pm similarity index 100% rename from lib/LazyPatricia.pm rename to lib/perl5/LazyPatricia.pm diff --git a/lib/NCLSorter.pm b/lib/perl5/NCLSorter.pm similarity index 100% rename from lib/NCLSorter.pm rename to lib/perl5/NCLSorter.pm diff --git a/lib/NCList.pm b/lib/perl5/NCList.pm similarity index 100% rename from lib/NCList.pm rename to lib/perl5/NCList.pm diff --git a/lib/NameHandler.pm b/lib/perl5/NameHandler.pm similarity index 100% rename from lib/NameHandler.pm rename to lib/perl5/NameHandler.pm diff --git a/lib/TiledImage.pm b/lib/perl5/TiledImage.pm similarity index 100% rename from lib/TiledImage.pm rename to lib/perl5/TiledImage.pm diff --git a/lib/TiledImage/DBPrimStorage.pm b/lib/perl5/TiledImage/DBPrimStorage.pm similarity index 100% rename from lib/TiledImage/DBPrimStorage.pm rename to lib/perl5/TiledImage/DBPrimStorage.pm diff --git a/lib/TiledImage/MemoryPrimStorage.pm b/lib/perl5/TiledImage/MemoryPrimStorage.pm similarity index 100% rename from lib/TiledImage/MemoryPrimStorage.pm rename to lib/perl5/TiledImage/MemoryPrimStorage.pm diff --git a/lib/TiledImage/demo-tiledimage.pl b/lib/perl5/TiledImage/demo-tiledimage.pl similarity index 100% rename from lib/TiledImage/demo-tiledimage.pl rename to lib/perl5/TiledImage/demo-tiledimage.pl diff --git a/lib/TiledImage/gdtile.sql b/lib/perl5/TiledImage/gdtile.sql similarity index 100% rename from lib/TiledImage/gdtile.sql rename to lib/perl5/TiledImage/gdtile.sql diff --git a/lib/TrackImage.pm b/lib/perl5/TrackImage.pm similarity index 100% rename from lib/TrackImage.pm rename to lib/perl5/TrackImage.pm