[med-svn] [Git][med-team/gatk][master] 3 commits: Correcting d/watch for new Github release page
Pierre Gruet
gitlab at salsa.debian.org
Mon Apr 19 19:16:27 BST 2021
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 <pgtdebian at free.fr> Fri, 25 Sep 2020 22:56:23 +0200
+ -- Pierre Gruet <pgt at debian.org> Sat, 17 Apr 2021 15:20:44 +0200
=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>,
- Pierre Gruet <pgtdebian at free.fr>
+ Pierre Gruet <pgt at debian.org>
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 <tille at debian.org>
-License: MIT
+ 2021 Pierre Gruet <pgt at debian.org>
+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
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