Ensembl · EbiArnie · Sep 20, 2024 · Sep 11, 2024 · Sep 11, 2024 · Sep 11, 2024
diff --git a/.travis.yml b/.travis.yml
@@ -33,7 +33,7 @@ before_install:
 
 install:
   - cpanm -v --sudo --notest XML::LibXML # https://github.com/shlomif/perl-XML-LibXML/pull/87
-  - cpanm -v --sudo --installdeps --with-all-features .
+  - cpanm -v --sudo --installdeps --notest --with-all-features .
   - cp travisci/MultiTestDB.conf.travisci.mysql  modules/t/MultiTestDB.conf.mysql
   - cp travisci/MultiTestDB.conf.travisci.SQLite modules/t/MultiTestDB.conf.SQLite
   - cp travisci/testdb.conf.travisci.mysql  testdb.conf.mysql

diff --git a/LICENSE b/LICENSE
@@ -1,4 +1,5 @@
-                                Apache License
+
+                                 Apache License
                            Version 2.0, January 2004
                         http://www.apache.org/licenses/
 
@@ -178,16 +179,15 @@
    APPENDIX: How to apply the Apache License to your work.
 
       To apply the Apache License to your work, attach the following
-      boilerplate notice, with the fields enclosed by brackets "{}"
+      boilerplate notice, with the fields enclosed by brackets "[]"
       replaced with your own identifying information. (Don't include
       the brackets!)  The text should be enclosed in the appropriate
       comment syntax for the file format. We also recommend that a
       file or class name and description of purpose be included on the
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-   Copyright [2016-2024] EMBL-European Bioinformatics Institute
+   Copyright [yyyy] [name of copyright owner]
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.
@@ -201,41 +201,3 @@
    See the License for the specific language governing permissions and
    limitations under the License.
 
-
-ENSEMBL CORE PROJECT SUBCOMPONENTS
-
-The Ensembl Core Project includes a number of subcomponents with
-separate copyright notices and license terms. Your use of the source
-code for the these subcomponents is subject to the terms and
-conditions of the following licenses.
-
-COMPONENT: modules/Bio/EnsEMBL/Utils/Cache.pm
-
-Code has been renamed from Tie::Cache to 
-Bio::EnsEMBL::Utils::Cache and originally distributed on CPAN.
-
-Copyright (c) 1999-2002 Joshua Chamas, Chamas Enterprises Inc.  
-Sponsored by development on NodeWorks http://www.nodeworks.com
-
-All rights reserved. This program is free software; 
-you can redistribute it and/or modify it under the same 
-terms as Perl itself.
-
-COMPONENT: misc-scripts/doxygen_filter/EnsEMBL/Filter.pm and 
-           misc-scripts/doxygen_filter/EnsEMBL/PerlFilter.pm. 
-
-Both portions of code were based on the following agreement; 
-PerlFilter.pm has seen significant re-writing but derives from the 
-original source.
-
-Doxygen Pre-Processor for Perl
-Copyright (C) 2002  Bart Schuller
-Copyright (C) 2006  Phinex Informatik AG
-All Rights Reserved
-
-Doxygen Filter is free software; you can redistribute it and/or modify
-it under the same terms as Perl itself.
-
-Larry Wall's 'Artistic License' for perl can be found in
-http://www.perl.com/pub/a/language/misc/Artistic.html
-
diff --git a/NOTICE b/NOTICE
@@ -0,0 +1,41 @@
+Ensembl
+Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
+
+This product includes software developed at:
+- EMBL-European Bioinformatics Institute
+- Wellcome Trust Sanger Institute
+
+ENSEMBL CORE PROJECT SUBCOMPONENTS
+
+The Ensembl Core Project includes a number of subcomponents with
+separate copyright notices and license terms. Your use of the source
+code for the these subcomponents is subject to the terms and
+conditions of the following licenses.
+
+COMPONENT: modules/Bio/EnsEMBL/Utils/Cache.pm
+
+Code has been renamed from Tie::Cache to 
+Bio::EnsEMBL::Utils::Cache and originally distributed on CPAN.
+
+Copyright (c) 1999-2002 Joshua Chamas, Chamas Enterprises Inc.  
+Sponsored by development on NodeWorks http://www.nodeworks.com
+
+All rights reserved. This program is free software; 
+you can redistribute it and/or modify it under the same 
+terms as Perl itself.
+
+COMPONENT: misc-scripts/doxygen_filter/EnsEMBL/Filter.pm and 
+           misc-scripts/doxygen_filter/EnsEMBL/PerlFilter.pm. 
+
+Both portions of code were based on the following agreement; 
+PerlFilter.pm has seen significant re-writing but derives from the 
+original source.
+
+Doxygen Pre-Processor for Perl
+Copyright (C) 2002  Bart Schuller
+Copyright (C) 2006  Phinex Informatik AG
+All Rights Reserved
+
+Doxygen Filter is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself.
diff --git a/misc-scripts/CreateFile4CopyDBoverServer.pl b/misc-scripts/CreateFile4CopyDBoverServer.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/alt_alleles/alt_alleles.pl b/misc-scripts/alt_alleles/alt_alleles.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/annual_copyright_updater.sh b/misc-scripts/annual_copyright_updater.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/AssemblyMapper/BlastzAligner.pm b/misc-scripts/assembly/AssemblyMapper/BlastzAligner.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
-Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2024] EMBL-European Bioinformatics Institute
+See the NOTICE file distributed with this work for additional information
+regarding copyright ownership.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/EXAMPLE.use_mapping.pl b/misc-scripts/assembly/EXAMPLE.use_mapping.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/align_by_clone_identity.pl b/misc-scripts/assembly/align_by_clone_identity.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/align_nonident_regions.pl b/misc-scripts/assembly/align_nonident_regions.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/align_nonident_regions_wrapper.pl b/misc-scripts/assembly/align_nonident_regions_wrapper.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/check_mapping.pl b/misc-scripts/assembly/check_mapping.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/cleanup_tmp_tables.sql b/misc-scripts/assembly/cleanup_tmp_tables.sql
@@ -1,5 +1,5 @@
--- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2024] EMBL-European Bioinformatics Institute
+-- See the NOTICE file distributed with this work for additional information
+-- regarding copyright ownership.
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/compare_assemblies.pl b/misc-scripts/assembly/compare_assemblies.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/conservation_statistics.pl b/misc-scripts/assembly/conservation_statistics.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/ensembl_assembly_to_chain.pl b/misc-scripts/assembly/ensembl_assembly_to_chain.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/exon_conservation_check.pl b/misc-scripts/assembly/exon_conservation_check.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/find_overlaps.pl b/misc-scripts/assembly/find_overlaps.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/fix_asm_overlaps.pl b/misc-scripts/assembly/fix_asm_overlaps.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/fix_cmp_overlaps.pl b/misc-scripts/assembly/fix_cmp_overlaps.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/fix_overlaps.pl b/misc-scripts/assembly/fix_overlaps.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/load_alternative_assembly.pl b/misc-scripts/assembly/load_alternative_assembly.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/load_feature_mappings.pl b/misc-scripts/assembly/load_feature_mappings.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/load_patch_fix_to_ref.pl b/misc-scripts/assembly/load_patch_fix_to_ref.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/mapping_stats.pl b/misc-scripts/assembly/mapping_stats.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/merge_cmp_gaps.pl b/misc-scripts/assembly/merge_cmp_gaps.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/assembly/test_assembly_mapping.pl b/misc-scripts/assembly/test_assembly_mapping.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/canonical_transcripts/emit_canonical_encodings.pl b/misc-scripts/canonical_transcripts/emit_canonical_encodings.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/canonical_transcripts/reason_changes.pl b/misc-scripts/canonical_transcripts/reason_changes.pl
@@ -1,5 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [2020-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/canonical_transcripts/select_canonical_transcripts.pl b/misc-scripts/canonical_transcripts/select_canonical_transcripts.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
-# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/misc-scripts/cloud/EnsCloud/Cmd.pm b/misc-scripts/cloud/EnsCloud/Cmd.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
-Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2024] EMBL-European Bioinformatics Institute
+See the NOTICE file distributed with this work for additional information
+regarding copyright ownership.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

diff --git a/misc-scripts/cloud/EnsCloud/Cmd/Command/SpeciesToVolumes.pm b/misc-scripts/cloud/EnsCloud/Cmd/Command/SpeciesToVolumes.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
-Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2024] EMBL-European Bioinformatics Institute
+See the NOTICE file distributed with this work for additional information
+regarding copyright ownership.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

diff --git a/misc-scripts/cloud/EnsCloud/Cmd/Command/list.pm b/misc-scripts/cloud/EnsCloud/Cmd/Command/list.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
-Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2024] EMBL-European Bioinformatics Institute
+See the NOTICE file distributed with this work for additional information
+regarding copyright ownership.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.