Skip to content

Commit 1f7fade

Browse files
droazenjonn-smith
droazen
and
jonn-smith
authored
Switch GATK to the Apache 2.0 license (#7079)
Switch GATK to the Apache 2.0 license Co-authored-by: Jonn Smith <jonn@broadinstitute.org>
1 parent 8f6c736 commit 1f7fade

File tree

8 files changed

+204
-95
lines changed

8 files changed

+204
-95
lines changed

‎LICENSE.TXT‎

Lines changed: 193 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -1,26 +1,193 @@
1-
Copyright (c) 2009-2020, Broad Institute, Inc. All rights reserved.
2-
3-
Redistribution and use in source and binary forms, with or without
4-
modification, are permitted provided that the following conditions are met:
5-
6-
* Redistributions of source code must retain the above copyright notice, this
7-
list of conditions and the following disclaimer.
8-
9-
* Redistributions in binary form must reproduce the above copyright notice,
10-
this list of conditions and the following disclaimer in the documentation
11-
and/or other materials provided with the distribution.
12-
13-
* Neither the name Broad Institute, Inc. nor the names of its
14-
contributors may be used to endorse or promote products derived from
15-
this software without specific prior written permission.
16-
17-
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
18-
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
19-
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
20-
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
21-
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
22-
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
23-
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
24-
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
25-
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
26-
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
1+
Copyright 2021 Broad Institute, Inc.
2+
3+
Licensed under the Apache License, Version 2.0 (the "License");
4+
you may not use this software except in compliance with the License.
5+
You may obtain a copy of the License at
6+
7+
http://www.apache.org/licenses/LICENSE-2.0
8+
9+
Unless required by applicable law or agreed to in writing, software
10+
distributed under the License is distributed on an "AS IS" BASIS,
11+
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12+
See the License for the specific language governing permissions and
13+
limitations under the License.
14+
15+
All files in the Genome Analysis Toolkit (GATK) (https://github.com/broadinstitute/gatk)
16+
are implicitly licensed under the Apache License, Version 2.0, unless otherwise explicitly stated.
17+
18+
Apache License
19+
Version 2.0, January 2004
20+
http://www.apache.org/licenses/
21+
22+
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
23+
24+
1. Definitions.
25+
26+
"License" shall mean the terms and conditions for use, reproduction,
27+
and distribution as defined by Sections 1 through 9 of this document.
28+
29+
"Licensor" shall mean the copyright owner or entity authorized by
30+
the copyright owner that is granting the License.
31+
32+
"Legal Entity" shall mean the union of the acting entity and all
33+
other entities that control, are controlled by, or are under common
34+
control with that entity. For the purposes of this definition,
35+
"control" means (i) the power, direct or indirect, to cause the
36+
direction or management of such entity, whether by contract or
37+
otherwise, or (ii) ownership of fifty percent (50%) or more of the
38+
outstanding shares, or (iii) beneficial ownership of such entity.
39+
40+
"You" (or "Your") shall mean an individual or Legal Entity
41+
exercising permissions granted by this License.
42+
43+
"Source" form shall mean the preferred form for making modifications,
44+
including but not limited to software source code, documentation
45+
source, and configuration files.
46+
47+
"Object" form shall mean any form resulting from mechanical
48+
transformation or translation of a Source form, including but
49+
not limited to compiled object code, generated documentation,
50+
and conversions to other media types.
51+
52+
"Work" shall mean the work of authorship, whether in Source or
53+
Object form, made available under the License, as indicated by a
54+
copyright notice that is included in or attached to the work
55+
(an example is provided in the Appendix below).
56+
57+
"Derivative Works" shall mean any work, whether in Source or Object
58+
form, that is based on (or derived from) the Work and for which the
59+
editorial revisions, annotations, elaborations, or other modifications
60+
represent, as a whole, an original work of authorship. For the purposes
61+
of this License, Derivative Works shall not include works that remain
62+
separable from, or merely link (or bind by name) to the interfaces of,
63+
the Work and Derivative Works thereof.
64+
65+
"Contribution" shall mean any work of authorship, including
66+
the original version of the Work and any modifications or additions
67+
to that Work or Derivative Works thereof, that is intentionally
68+
submitted to Licensor for inclusion in the Work by the copyright owner
69+
or by an individual or Legal Entity authorized to submit on behalf of
70+
the copyright owner. For the purposes of this definition, "submitted"
71+
means any form of electronic, verbal, or written communication sent
72+
to the Licensor or its representatives, including but not limited to
73+
communication on electronic mailing lists, source code control systems,
74+
and issue tracking systems that are managed by, or on behalf of, the
75+
Licensor for the purpose of discussing and improving the Work, but
76+
excluding communication that is conspicuously marked or otherwise
77+
designated in writing by the copyright owner as "Not a Contribution."
78+
79+
"Contributor" shall mean Licensor and any individual or Legal Entity
80+
on behalf of whom a Contribution has been received by Licensor and
81+
subsequently incorporated within the Work.
82+
83+
2. Grant of Copyright License. Subject to the terms and conditions of
84+
this License, each Contributor hereby grants to You a perpetual,
85+
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
86+
copyright license to reproduce, prepare Derivative Works of,
87+
publicly display, publicly perform, sublicense, and distribute the
88+
Work and such Derivative Works in Source or Object form.
89+
90+
3. Grant of Patent License. Subject to the terms and conditions of
91+
this License, each Contributor hereby grants to You a perpetual,
92+
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
93+
(except as stated in this section) patent license to make, have made,
94+
use, offer to sell, sell, import, and otherwise transfer the Work,
95+
where such license applies only to those patent claims licensable
96+
by such Contributor that are necessarily infringed by their
97+
Contribution(s) alone or by combination of their Contribution(s)
98+
with the Work to which such Contribution(s) was submitted. If You
99+
institute patent litigation against any entity (including a
100+
cross-claim or counterclaim in a lawsuit) alleging that the Work
101+
or a Contribution incorporated within the Work constitutes direct
102+
or contributory patent infringement, then any patent licenses
103+
granted to You under this License for that Work shall terminate
104+
as of the date such litigation is filed.
105+
106+
4. Redistribution. You may reproduce and distribute copies of the
107+
Work or Derivative Works thereof in any medium, with or without
108+
modifications, and in Source or Object form, provided that You
109+
meet the following conditions:
110+
111+
(a) You must give any other recipients of the Work or
112+
Derivative Works a copy of this License; and
113+
114+
(b) You must cause any modified files to carry prominent notices
115+
stating that You changed the files; and
116+
117+
(c) You must retain, in the Source form of any Derivative Works
118+
that You distribute, all copyright, patent, trademark, and
119+
attribution notices from the Source form of the Work,
120+
excluding those notices that do not pertain to any part of
121+
the Derivative Works; and
122+
123+
(d) If the Work includes a "NOTICE" text file as part of its
124+
distribution, then any Derivative Works that You distribute must
125+
include a readable copy of the attribution notices contained
126+
within such NOTICE file, excluding those notices that do not
127+
pertain to any part of the Derivative Works, in at least one
128+
of the following places: within a NOTICE text file distributed
129+
as part of the Derivative Works; within the Source form or
130+
documentation, if provided along with the Derivative Works; or,
131+
within a display generated by the Derivative Works, if and
132+
wherever such third-party notices normally appear. The contents
133+
of the NOTICE file are for informational purposes only and
134+
do not modify the License. You may add Your own attribution
135+
notices within Derivative Works that You distribute, alongside
136+
or as an addendum to the NOTICE text from the Work, provided
137+
that such additional attribution notices cannot be construed
138+
as modifying the License.
139+
140+
You may add Your own copyright statement to Your modifications and
141+
may provide additional or different license terms and conditions
142+
for use, reproduction, or distribution of Your modifications, or
143+
for any such Derivative Works as a whole, provided Your use,
144+
reproduction, and distribution of the Work otherwise complies with
145+
the conditions stated in this License.
146+
147+
5. Submission of Contributions. Unless You explicitly state otherwise,
148+
any Contribution intentionally submitted for inclusion in the Work
149+
by You to the Licensor shall be under the terms and conditions of
150+
this License, without any additional terms or conditions.
151+
Notwithstanding the above, nothing herein shall supersede or modify
152+
the terms of any separate license agreement you may have executed
153+
with Licensor regarding such Contributions.
154+
155+
6. Trademarks. This License does not grant permission to use the trade
156+
names, trademarks, service marks, or product names of the Licensor,
157+
except as required for reasonable and customary use in describing the
158+
origin of the Work and reproducing the content of the NOTICE file.
159+
160+
7. Disclaimer of Warranty. Unless required by applicable law or
161+
agreed to in writing, Licensor provides the Work (and each
162+
Contributor provides its Contributions) on an "AS IS" BASIS,
163+
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
164+
implied, including, without limitation, any warranties or conditions
165+
of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
166+
PARTICULAR PURPOSE. You are solely responsible for determining the
167+
appropriateness of using or redistributing the Work and assume any
168+
risks associated with Your exercise of permissions under this License.
169+
170+
8. Limitation of Liability. In no event and under no legal theory,
171+
whether in tort (including negligence), contract, or otherwise,
172+
unless required by applicable law (such as deliberate and grossly
173+
negligent acts) or agreed to in writing, shall any Contributor be
174+
liable to You for damages, including any direct, indirect, special,
175+
incidental, or consequential damages of any character arising as a
176+
result of this License or out of the use or inability to use the
177+
Work (including but not limited to damages for loss of goodwill,
178+
work stoppage, computer failure or malfunction, or any and all
179+
other commercial damages or losses), even if such Contributor
180+
has been advised of the possibility of such damages.
181+
182+
9. Accepting Warranty or Additional Liability. While redistributing
183+
the Work or Derivative Works thereof, You may choose to offer,
184+
and charge a fee for, acceptance of support, warranty, indemnity,
185+
or other liability obligations and/or rights consistent with this
186+
License. However, in accepting such obligations, You may act only
187+
on Your own behalf and on Your sole responsibility, not on behalf
188+
of any other Contributor, and only if You agree to indemnify,
189+
defend, and hold each Contributor harmless for any liability
190+
incurred by, or claims asserted against, such Contributor by reason
191+
of your accepting any such warranty or additional liability.
192+
193+
END OF TERMS AND CONDITIONS

‎README.md‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,13 @@
11
[![Build Status](https://travis-ci.com/broadinstitute/gatk.svg?branch=master)](https://travis-ci.com/broadinstitute/gatk)
22
[![Maven Central](https://img.shields.io/maven-central/v/org.broadinstitute/gatk.svg)](https://maven-badges.herokuapp.com/maven-central/org.broadinstitute/gatk)
3-
[![License (3-Clause BSD)](https://img.shields.io/badge/license-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
3+
[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
44

55
***Please see the [GATK website](http://www.broadinstitute.org/gatk), where you can download a precompiled executable, read documentation, ask questions, and receive technical support. For GitHub basics, see [here](https://software.broadinstitute.org/gatk/documentation/article?id=23405).***
66

77
### GATK 4
88

99
This repository contains the next generation of the Genome Analysis Toolkit (GATK). The contents
10-
of this repository are 100% open source and released under the BSD 3-Clause license (see [LICENSE.TXT](https://github.com/broadinstitute/gatk/blob/master/LICENSE.TXT)).
10+
of this repository are 100% open source and released under the Apache 2.0 license (see [LICENSE.TXT](https://github.com/broadinstitute/gatk/blob/master/LICENSE.TXT)).
1111

1212
GATK4 aims to bring together well-established tools from the [GATK](http://www.broadinstitute.org/gatk) and
1313
[Picard](http://broadinstitute.github.io/picard/) codebases under a streamlined framework,
@@ -368,7 +368,7 @@ echo "source <PATH_TO>/gatk-completion.sh" >> ~/.bashrc
368368
369369
* **Try to keep datafiles under 100kb in size.** Larger test files should go into `src/test/resources/large` (and subdirectories) so that they'll be stored and tracked by git-lfs as described [above](#lfs).
370370
371-
* GATK4 is BSD licensed. The license is in the top level LICENSE.TXT file. Do not add any additional license text or accept files with a license included in them.
371+
* GATK4 is Apache 2.0 licensed. The license is in the top level LICENSE.TXT file. Do not add any additional license text or accept files with a license included in them.
372372
373373
* Each tool should have at least one good end-to-end integration test with a check for expected output, plus high-quality unit tests for all non-trivial utility methods/classes used by the tool. Although we have no specific coverage target, coverage should be extensive enough that if tests pass, the tool is guaranteed to be in a usable state.
374374
@@ -643,4 +643,4 @@ The authors list is maintained in the [AUTHORS](https://github.com/broadinstitut
643643
See also the [Contributors](https://github.com/broadinstitute/gatk/graphs/contributors) list at github.
644644
645645
## <a name="license">License</a>
646-
Licensed under the BSD License. See the [LICENSE.txt](https://github.com/broadinstitute/gatk/blob/master/LICENSE.TXT) file.
646+
Licensed under the Apache 2.0 License. See the [LICENSE.txt](https://github.com/broadinstitute/gatk/blob/master/LICENSE.TXT) file.

‎build.gradle‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -907,7 +907,7 @@ def basePomConfiguration = {
907907

908908
licenses {
909909
license {
910-
name 'BSD 3-Clause'
910+
name 'Apache 2.0'
911911
url 'https://github.com/broadinstitute/gatk/blob/master/LICENSE.TXT'
912912
distribution 'repo'
913913
}

‎scripts/cnn_variant_wdl/README.md‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -62,7 +62,7 @@ view the following tutorial [(How to) Execute Workflows from the gatk-workflows
6262
- The following material is provided by the Data Science Platforum group at the Broad Institute. Please direct any questions or concerns to one of our forum sites : [GATK](https://gatk.broadinstitute.org/hc/en-us/community/topics) or [Terra](https://support.terra.bio/hc/en-us/community/topics/360000500432).
6363

6464
### LICENSING :
65-
This script is released under the WDL source code license (BSD-3) (see LICENSE in
66-
https://github.com/broadinstitute/wdl). Note however that the programs it calls may
65+
This script is released under the GATK source code license (Apache 2.0) (see LICENSE in
66+
https://github.com/broadinstitute/gatk). Note however that the programs it calls may
6767
be subject to different licenses. Users are responsible for checking that they are
6868
authorized to run all programs before running this script.

‎scripts/mutect2_wdl/mutect2.wdl‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -60,13 +60,14 @@ version 1.0
6060
## - Successfully tested on v34
6161
##
6262
## LICENSING :
63-
## This script is released under the WDL source code license (BSD-3) (see LICENSE in
64-
## https://github.com/broadinstitute/wdl). Note however that the programs it calls may
63+
## This script is released under the GATK source code license (Apache 2.0) (see LICENSE in
64+
## https://github.com/broadinstitute/gatk). Note however that the programs it calls may
6565
## be subject to different licenses. Users are responsible for checking that they are
66-
## authorized to run all programs before running this script. Please see the docker
66+
## authorized to run all programs before running this script. Please see the docker
6767
## pages at https://hub.docker.com/r/broadinstitute/* for detailed licensing information
6868
## pertaining to the included programs.
6969
70+
7071
struct Runtime {
7172
String gatk_docker
7273
File? gatk_override

‎src/main/java/org/broadinstitute/hellbender/tools/funcotator/AminoAcid.java‎

Lines changed: 0 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -1,28 +1,3 @@
1-
/*
2-
* Copyright 2012-2016 Broad Institute, Inc.
3-
*
4-
* Permission is hereby granted, free of charge, to any person
5-
* obtaining a copy of this software and associated documentation
6-
* files (the "Software"), to deal in the Software without
7-
* restriction, including without limitation the rights to use,
8-
* copy, modify, merge, publish, distribute, sublicense, and/or sell
9-
* copies of the Software, and to permit persons to whom the
10-
* Software is furnished to do so, subject to the following
11-
* conditions:
12-
*
13-
* The above copyright notice and this permission notice shall be
14-
* included in all copies or substantial portions of the Software.
15-
*
16-
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
17-
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
18-
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
19-
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
20-
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
21-
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
22-
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
23-
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
24-
*/
25-
261
package org.broadinstitute.hellbender.tools.funcotator;
272

283
public enum AminoAcid {

‎src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/CompOverlap.java‎

Lines changed: 0 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -8,15 +8,6 @@
88
import org.broadinstitute.hellbender.tools.walkers.varianteval.util.Analysis;
99
import org.broadinstitute.hellbender.tools.walkers.varianteval.util.DataPoint;
1010

11-
/**
12-
* The Broad Institute
13-
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
14-
* This software and its documentation are copyright 2009 by the
15-
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
16-
* <p/>
17-
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
18-
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
19-
*/
2011
@Analysis(description = "The overlap between eval and comp sites")
2112
public class CompOverlap extends VariantEvaluator implements StandardEval {
2213
@DataPoint(description = "number of eval variant sites", format = "%d")

0 commit comments

Comments
 (0)