diff --git a/LICENSE.TXT b/LICENSE.TXT index 03e04701511..814463714a3 100644 --- a/LICENSE.TXT +++ b/LICENSE.TXT @@ -1,26 +1,193 @@ -Copyright (c) 2009-2020, Broad Institute, Inc. 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However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS diff --git a/README.md b/README.md index 6a2f913427d..13fd4649849 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,13 @@ [![Build Status](https://travis-ci.com/broadinstitute/gatk.svg?branch=master)](https://travis-ci.com/broadinstitute/gatk) [![Maven Central](https://img.shields.io/maven-central/v/org.broadinstitute/gatk.svg)](https://maven-badges.herokuapp.com/maven-central/org.broadinstitute/gatk) -[![License (3-Clause BSD)](https://img.shields.io/badge/license-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause) +[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) ***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).*** ### GATK 4 This repository contains the next generation of the Genome Analysis Toolkit (GATK). The contents -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)). +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)). GATK4 aims to bring together well-established tools from the [GATK](http://www.broadinstitute.org/gatk) and [Picard](http://broadinstitute.github.io/picard/) codebases under a streamlined framework, @@ -368,7 +368,7 @@ echo "source /gatk-completion.sh" >> ~/.bashrc * **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). -* 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. +* 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. * 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. @@ -643,4 +643,4 @@ The authors list is maintained in the [AUTHORS](https://github.com/broadinstitut See also the [Contributors](https://github.com/broadinstitute/gatk/graphs/contributors) list at github. ## License -Licensed under the BSD License. See the [LICENSE.txt](https://github.com/broadinstitute/gatk/blob/master/LICENSE.TXT) file. +Licensed under the Apache 2.0 License. See the [LICENSE.txt](https://github.com/broadinstitute/gatk/blob/master/LICENSE.TXT) file. diff --git a/build.gradle b/build.gradle index 2a882181cca..274334652d5 100644 --- a/build.gradle +++ b/build.gradle @@ -907,7 +907,7 @@ def basePomConfiguration = { licenses { license { - name 'BSD 3-Clause' + name 'Apache 2.0' url 'https://github.com/broadinstitute/gatk/blob/master/LICENSE.TXT' distribution 'repo' } diff --git a/scripts/cnn_variant_wdl/README.md b/scripts/cnn_variant_wdl/README.md index 52e3fe56a55..e3b19930d4b 100644 --- a/scripts/cnn_variant_wdl/README.md +++ b/scripts/cnn_variant_wdl/README.md @@ -62,7 +62,7 @@ view the following tutorial [(How to) Execute Workflows from the gatk-workflows - 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). ### LICENSING : - This script is released under the WDL source code license (BSD-3) (see LICENSE in - https://github.com/broadinstitute/wdl). Note however that the programs it calls may + This script is released under the GATK source code license (Apache 2.0) (see LICENSE in + https://github.com/broadinstitute/gatk). Note however that the programs it calls may be subject to different licenses. Users are responsible for checking that they are authorized to run all programs before running this script. diff --git a/scripts/mutect2_wdl/mutect2.wdl b/scripts/mutect2_wdl/mutect2.wdl index 40da47fd05b..1d02f9fb45e 100755 --- a/scripts/mutect2_wdl/mutect2.wdl +++ b/scripts/mutect2_wdl/mutect2.wdl @@ -60,13 +60,14 @@ version 1.0 ## - Successfully tested on v34 ## ## LICENSING : -## This script is released under the WDL source code license (BSD-3) (see LICENSE in -## https://github.com/broadinstitute/wdl). Note however that the programs it calls may +## This script is released under the GATK source code license (Apache 2.0) (see LICENSE in +## https://github.com/broadinstitute/gatk). Note however that the programs it calls may ## be subject to different licenses. Users are responsible for checking that they are -## authorized to run all programs before running this script. Please see the docker +## authorized to run all programs before running this script. Please see the docker ## pages at https://hub.docker.com/r/broadinstitute/* for detailed licensing information ## pertaining to the included programs. + struct Runtime { String gatk_docker File? gatk_override diff --git a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/AminoAcid.java b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/AminoAcid.java index 7f811824d95..4ffc48fa02d 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/AminoAcid.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/AminoAcid.java @@ -1,28 +1,3 @@ -/* -* Copyright 2012-2016 Broad Institute, Inc. -* -* Permission is hereby granted, free of charge, to any person -* obtaining a copy of this software and associated documentation -* files (the "Software"), to deal in the Software without -* restriction, including without limitation the rights to use, -* copy, modify, merge, publish, distribute, sublicense, and/or sell -* copies of the Software, and to permit persons to whom the -* Software is furnished to do so, subject to the following -* conditions: -* -* The above copyright notice and this permission notice shall be -* included in all copies or substantial portions of the Software. -* -* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, -* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES -* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND -* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT -* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, -* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR -* THE USE OR OTHER DEALINGS IN THE SOFTWARE. -*/ - package org.broadinstitute.hellbender.tools.funcotator; public enum AminoAcid { diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/CompOverlap.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/CompOverlap.java index 0647b4342a9..5390f716095 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/CompOverlap.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/CompOverlap.java @@ -8,15 +8,6 @@ import org.broadinstitute.hellbender.tools.walkers.varianteval.util.Analysis; import org.broadinstitute.hellbender.tools.walkers.varianteval.util.DataPoint; -/** - * The Broad Institute - * SOFTWARE COPYRIGHT NOTICE AGREEMENT - * This software and its documentation are copyright 2009 by the - * Broad Institute/Massachusetts Institute of Technology. All rights are reserved. - *

- * This software is supplied without any warranty or guaranteed support whatsoever. Neither - * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality. - */ @Analysis(description = "The overlap between eval and comp sites") public class CompOverlap extends VariantEvaluator implements StandardEval { @DataPoint(description = "number of eval variant sites", format = "%d") diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/SnpEffUtilUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/SnpEffUtilUnitTest.java index 9a7acba1b5c..68a1f993c9e 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/SnpEffUtilUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/SnpEffUtilUnitTest.java @@ -1,28 +1,3 @@ -/* -* Copyright 2012-2016 Broad Institute, Inc. -* -* Permission is hereby granted, free of charge, to any person -* obtaining a copy of this software and associated documentation -* files (the "Software"), to deal in the Software without -* restriction, including without limitation the rights to use, -* copy, modify, merge, publish, distribute, sublicense, and/or sell -* copies of the Software, and to permit persons to whom the -* Software is furnished to do so, subject to the following -* conditions: -* -* The above copyright notice and this permission notice shall be -* included in all copies or substantial portions of the Software. -* -* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, -* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES -* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND -* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT -* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, -* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR -* THE USE OR OTHER DEALINGS IN THE SOFTWARE. -*/ - package org.broadinstitute.hellbender.tools.walkers.varianteval.util; /**