Commit 61deb3f4 authored by Leo Gordon's avatar Leo Gordon
Browse files

added Apache 2.0 license to all files

parent a55a3d94
=pod =pod
=head1 NAME =head1 NAME
...@@ -25,12 +24,26 @@ ...@@ -25,12 +24,26 @@
Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.
=head1 CONTACT =head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions. Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut =cut
package MiniPecanMulti_conf; package MiniPecanMulti_conf;
use strict; use strict;
......
=pod =pod
=head1 NAME =head1 NAME
...@@ -25,12 +24,26 @@ ...@@ -25,12 +24,26 @@
Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.
=head1 CONTACT =head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions. Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut =cut
package MiniPecanSingle2_conf; package MiniPecanSingle2_conf;
use strict; use strict;
......
=pod =pod
=head1 NAME =head1 NAME
...@@ -25,12 +24,26 @@ ...@@ -25,12 +24,26 @@
Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.
=head1 CONTACT =head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions. Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut =cut
package MiniPecanSingle3_conf; package MiniPecanSingle3_conf;
use strict; use strict;
......
=pod =pod
=head1 NAME =head1 NAME
...@@ -25,12 +24,26 @@ ...@@ -25,12 +24,26 @@
Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.
=head1 CONTACT =head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions. Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut =cut
package MiniPecanSingle_conf; package MiniPecanSingle_conf;
use strict; use strict;
......
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod =pod
=head1 NAME =head1 NAME
...@@ -49,14 +44,22 @@ ...@@ -49,14 +44,22 @@
It is also responsible for interfacing with the Queen to identify workers which died It is also responsible for interfacing with the Queen to identify workers which died
unexpectantly so that she can free the dead workers unfinished jobs. unexpectantly so that she can free the dead workers unfinished jobs.
=head1 CONTACT =head1 LICENSE
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions. Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
You may obtain a copy of the License at
=head1 APPENDIX http://www.apache.org/licenses/LICENSE-2.0
The rest of the documentation details each of the object methods. Unless required by applicable law or agreed to in writing, software distributed under the License
Internal methods are usually preceded with a _ is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.
=head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut =cut
......
...@@ -4,19 +4,31 @@ ...@@ -4,19 +4,31 @@
Bio::EnsEMBL::Hive::Accumulator Bio::EnsEMBL::Hive::Accumulator
=head1 SYNOPSIS
=head1 DESCRIPTION =head1 DESCRIPTION
A data container object that defines parameters for accumulated dataflow. A data container object that defines parameters for accumulated dataflow.
This object is generated from specially designed datalow URLs. This object is generated from specially designed datalow URLs.
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.
=head1 CONTACT =head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions. Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut =cut
package Bio::EnsEMBL::Hive::Accumulator; package Bio::EnsEMBL::Hive::Accumulator;
use strict; use strict;
......
...@@ -4,8 +4,6 @@ ...@@ -4,8 +4,6 @@
Bio::EnsEMBL::Hive::Analysis Bio::EnsEMBL::Hive::Analysis
=head1 SYNOPSIS
=head1 DESCRIPTION =head1 DESCRIPTION
An Analysis object represents a "stage" of the Hive pipeline that groups together An Analysis object represents a "stage" of the Hive pipeline that groups together
...@@ -15,12 +13,26 @@ ...@@ -15,12 +13,26 @@
Control rules unblock when their condition Analyses are done. Control rules unblock when their condition Analyses are done.
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.
=head1 CONTACT =head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions. Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut =cut
package Bio::EnsEMBL::Hive::Analysis; package Bio::EnsEMBL::Hive::Analysis;
use strict; use strict;
......
# Perl module for Bio::EnsEMBL::Hive::AnalysisCtrlRule
#
# Creator: Jessica Severin <jessica@ebi.ac.uk>
# Date of creation: 22.03.2004
#
# Copyright EMBL-EBI 2000-2004
#
# You may distribute this module under the same terms as perl itself
=pod =pod
=head1 NAME =head1 NAME
Bio::EnsEMBL::Hive::AnalysisCtrlRule Bio::EnsEMBL::Hive::AnalysisCtrlRule
=head1 SYNOPSIS
=head1 DESCRIPTION =head1 DESCRIPTION
An 'analysis control rule' is a high level blocking control structure where there is An 'analysis control rule' is a high level blocking control structure where there is
...@@ -25,6 +14,18 @@ ...@@ -25,6 +14,18 @@
Allows the 'condition' analysis to be specified with a network savy URL like Allows the 'condition' analysis to be specified with a network savy URL like
mysql://ensadmin:<pass>@ecs2:3361/compara_hive_test?analysis.logic_name='blast_NCBI34' mysql://ensadmin:<pass>@ecs2:3361/compara_hive_test?analysis.logic_name='blast_NCBI34'
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.
=head1 CONTACT =head1 CONTACT
...@@ -38,7 +39,6 @@ ...@@ -38,7 +39,6 @@
=cut =cut
package Bio::EnsEMBL::Hive::AnalysisCtrlRule; package Bio::EnsEMBL::Hive::AnalysisCtrlRule;
use strict; use strict;
......
#
# You may distribute this module under the same terms as perl itself
=pod =pod
=head1 NAME =head1 NAME
...@@ -12,6 +9,19 @@ ...@@ -12,6 +9,19 @@
An AnalysisJob is the link between the input_id control data, the analysis and An AnalysisJob is the link between the input_id control data, the analysis and
the rule system. It also tracks the state of the job as it is processed the rule system. It also tracks the state of the job as it is processed
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.
=head1 CONTACT =head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions. Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
......
#
# You may distribute this module under the same terms as perl itself
=pod =pod
=head1 NAME =head1 NAME
Bio::EnsEMBL::Hive::AnalysisStats Bio::EnsEMBL::Hive::AnalysisStats
=head1 SYNOPSIS
=head1 DESCRIPTION =head1 DESCRIPTION
An object that maintains counters for jobs in different states. This data is used by the Scheduler.
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.
=head1 CONTACT =head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions. Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
......
# A base class for objects that we want to be configurable in the following sense: =pod
# 1) have a pointer to the $config
# 2) know their context =head1 NAME
# 3) automatically apply that context when getting and setting
Bio::EnsEMBL::Hive::Configurable
=head1 DESCRIPTION
A base class for objects that we want to be configurable in the following sense:
1) have a pointer to the $config
2) know their context
3) automatically apply that context when getting and setting
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.
=head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut
package Bio::EnsEMBL::Hive::Configurable; package Bio::EnsEMBL::Hive::Configurable;
......
...@@ -12,6 +12,19 @@ ...@@ -12,6 +12,19 @@
This is currently an "objectless" adaptor for building accumulated structures. This is currently an "objectless" adaptor for building accumulated structures.
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.
=head1 CONTACT =head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions. Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
......
...@@ -15,6 +15,19 @@ ...@@ -15,6 +15,19 @@
Module to encapsulate all db access for persistent class Analysis. Module to encapsulate all db access for persistent class Analysis.
There should be just one such adaptor per application and database connection. There should be just one such adaptor per application and database connection.
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.
=head1 CONTACT =head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions. Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
......
...@@ -14,6 +14,19 @@ ...@@ -14,6 +14,19 @@
Module to encapsulate all db access for persistent class AnalysisCtrlRule. Module to encapsulate all db access for persistent class AnalysisCtrlRule.
There should be just one per application and database connection. There should be just one per application and database connection.
=head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.
=head1 CONTACT =head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions. Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
......
# Perl module for Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor
#
# Date of creation: 22.03.2004
# Original Creator : Jessica Severin <jessica@ebi.ac.uk>
#
# Copyright EMBL-EBI 2004
#
# You may distribute this module under the same terms as perl itself
=pod =pod
=head1 NAME =head1 NAME
...@@ -19,10 +10,21 @@ ...@@ -19,10 +10,21 @@
=head1 DESCRIPTION =head1 DESCRIPTION
analysis_data table holds LONGTEXT data for use by the analysis system. analysis_data table holds LONGTEXT data that is currently used as an extension of some fixed-width fields of 'job' table.
This data is general purpose and it's up to each analysis to It is no longer general-purpose. Please avoid accessing this table directly or via the adaptor.
determine how to use it.
This Adaptor module is used to access/store this data. =head1 LICENSE
Copyright [1999-2013] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.
=head1 CONTACT