Pierre Gruet pushed to branch master at Debian Med / gatk
Commits: da0ea9e6 by Pierre Gruet at 2021-04-17T15:18:40+02:00 Correcting d/watch for new Github release page - - - - - 05e09eb3 by Pierre Gruet at 2021-04-17T15:19:32+02:00 Revising d/copyright for the new release - - - - - 51147ece by Pierre Gruet at 2021-04-17T15:21:16+02:00 Preparing to build from upstream version 4.2.0.0+dfsg - - - - - 4 changed files: - debian/changelog - debian/control - debian/copyright - debian/watch Changes: ===================================== debian/changelog ===================================== @@ -1,5 +1,5 @@ -gatk (4.1.8.1+dfsg-1) UNRELEASED; urgency=medium +gatk (4.2.0.0+dfsg-1) UNRELEASED; urgency=medium * Initial release (Closes: #<bug>) - -- Pierre Gruet <[email protected]> Fri, 25 Sep 2020 22:56:23 +0200 + -- Pierre Gruet <[email protected]> Sat, 17 Apr 2021 15:20:44 +0200 ===================================== debian/control ===================================== @@ -3,7 +3,7 @@ Section: science Priority: optional Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Andreas Tille <[email protected]>, - Pierre Gruet <[email protected]> + Pierre Gruet <[email protected]> Build-Depends: debhelper-compat (= 13), default-jdk, gradle-debian-helper ===================================== debian/copyright ===================================== @@ -1,39 +1,56 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: GATK Source: https://github.com/broadgsa/gatk/ -Files-Excluded: *.data - .github +Files-Excluded: .github .gitignore .gitattributes .dockerignore gradle + scripts/funcotator/data_sources/getOreganno.py + scripts/funcotator/data_sources/TableParser.py + scripts/funcotator/data_sources/cosmic/*.py +Comment: We remove gradle/ as it contains a jar. In the scripts/ subdirs listed + above there are files with unclear copyright or with non-free licenses. Files: * -Copyright: 2012-2014 The Broad Institute -License: MIT +Copyright: 2017-2021 Broad Institute, Inc. +License: Apache-2.0 Files: debian/* Copyright: 2015 Andreas Tille <[email protected]> -License: MIT + 2021 Pierre Gruet <[email protected]> +License: Apache-2.0 -License: MIT - 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: +Files: src/main/python/org/broadinstitute/hellbender/gcnvkernel/* +Copyright: 2009-2018 Broad Institute, Inc. +License: BSD-3-clause + +License: Apache-2.0 +On Debian systems the full text of the Apache-2.0 license can be found in + /usr/share/common-licenses/Apache-2.0. + +License: BSD-3-clause + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are met: + . + * Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + . + * Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. . - The above copyright notice and this permission notice shall be - included in all copies or substantial portions of the Software. + * Neither the name Broad Institute, Inc. nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. . - 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. + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE + FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL + DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR + SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER + CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ===================================== debian/watch ===================================== @@ -1,4 +1,4 @@ version=4 opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \ - https://github.com/broadinstitute/gatk/releases .*/archive/(\d[.\d]+)@ARCHIVE_EXT@ + https://github.com/broadinstitute/gatk/releases (?:.*?/)?v?(\d[.\d]*)@ARCHIVE_EXT@ View it on GitLab: https://salsa.debian.org/med-team/gatk/-/compare/aa7a3a3804e4d4e22a1bad5ec83dfbacabf3e663...51147ece5208ef358502c87f9698e4490f149994 -- View it on GitLab: https://salsa.debian.org/med-team/gatk/-/compare/aa7a3a3804e4d4e22a1bad5ec83dfbacabf3e663...51147ece5208ef358502c87f9698e4490f149994 You're receiving this email because of your account on salsa.debian.org.
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