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commit 023d7a17593fd19e8b9c1c8e72189ca50796b0b6 Author: Vincent Danjean <[email protected]> Date: Sat Sep 5 23:48:15 2015 +0200 Update package with new upstream web site * fix debian/watch * use debian/copyright to remove convenience binary jar files --- debian/README.source | 7 +++ debian/control | 5 +- debian/copyright | 175 ++------------------------------------------------- debian/rules | 17 ----- debian/watch | 3 +- 5 files changed, 16 insertions(+), 191 deletions(-) diff --git a/debian/README.source b/debian/README.source index 602c48a..a2134ef 100644 --- a/debian/README.source +++ b/debian/README.source @@ -1,3 +1,10 @@ +Upstream is using GitHub. debian/watch has been updated and debian/copyright +is used to removed convenience prebuilt jar from the tarball. +Sources are also reorganized and some of them have been moved to the new +htsjdk package. + + -- Vincent Danjean <[email protected]> 2015-09-05 + It seems that upstream are moving to GitHub, next release should be available in Github repo. See comment at: http://sourceforge.net/projects/picard/files/picard-tools/1.113/ diff --git a/debian/control b/debian/control index f06996f..ddf3f96 100644 --- a/debian/control +++ b/debian/control @@ -2,7 +2,8 @@ Source: picard-tools Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Shaun Jackman <[email protected]>, Charles Plessy <[email protected]>, - Olivier Sallou <[email protected]> + Olivier Sallou <[email protected]>, + Vincent Danjean <[email protected]> Section: science Priority: optional Build-Depends: ant, @@ -18,7 +19,7 @@ Build-Depends: ant, Standards-Version: 3.9.6 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/picard-tools.git Vcs-Git: git://anonscm.debian.org/debian-med/picard-tools.git -Homepage: http://picard.sourceforge.net/ +Homepage: http://broadinstitute.github.io/picard/ Package: libsam-java Architecture: all diff --git a/debian/copyright b/debian/copyright index 898b341..fc167ee 100644 --- a/debian/copyright +++ b/debian/copyright @@ -1,6 +1,7 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ -Source: http://picard.svn.sourceforge.net/viewvc/picard/tags/1.110/ -Comment: Some source files are removed, see debian/rules. +Source: https://github.com/broadinstitute/picard/releases +Comment: Convenience binary jar files are removed. +Files-Excluded: lib/* Files: * Copyright: © 2009–2014 The Broad Institute @@ -23,59 +24,6 @@ License: MIT OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. -Files: src/java/net/sf/samtools/util/DateParser.java -Copyright: 2000 MIT, INRIA and Keio -License: W3C-Software - W3C IPR SOFTWARE NOTICE - . - Copyright 1995-1998 World Wide Web Consortium, (Massachusetts Institute of - Technology, Institut National de Recherche en Informatique et en - Automatique, Keio University). All Rights Reserved. - http://www.w3.org/Consortium/Legal/ - . - This W3C work (including software, documents, or other related items) is - being provided by the copyright holders under the following license. By - obtaining, using and/or copying this work, you (the licensee) agree that you - have read, understood, and will comply with the following terms and - conditions: - . - Permission to use, copy, and modify this software and its documentation, - with or without modification, for any purpose and without fee or royalty is - hereby granted, provided that you include the following on ALL copies of the - software and documentation or portions thereof, including modifications, - that you make: - . - 1. The full text of this NOTICE in a location viewable to users of the - redistributed or derivative work. - 2. Any pre-existing intellectual property disclaimers, notices, or terms - and conditions. If none exist, a short notice of the following form - (hypertext is preferred, text is permitted) should be used within the - body of any redistributed or derivative code: "Copyright World Wide - Web Consortium, (Massachusetts Institute of Technology, Institut - National de Recherche en Informatique et en Automatique, Keio - University). All Rights Reserved. http://www.w3.org/Consortium/Legal/"; - 3. Notice of any changes or modifications to the W3C files, including the - date changes were made. (We recommend you provide URIs to the location - from which the code is derived). - . - In addition, creators of derivitive works must include the full text of this - NOTICE in a location viewable to users of the derivitive work. - . - THIS SOFTWARE AND DOCUMENTATION IS PROVIDED "AS IS," AND COPYRIGHT HOLDERS - MAKE NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED, INCLUDING BUT NOT - LIMITED TO, WARRANTIES OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR - PURPOSE OR THAT THE USE OF THE SOFTWARE OR DOCUMENTATION WILL NOT INFRINGE - ANY THIRD PARTY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. - . - COPYRIGHT HOLDERS WILL NOT BE LIABLE FOR ANY DIRECT, INDIRECT, SPECIAL OR - CONSEQUENTIAL DAMAGES ARISING OUT OF ANY USE OF THE SOFTWARE OR - DOCUMENTATION. - . - The name and trademarks of copyright holders may NOT be used in advertising - or publicity pertaining to the software without specific, written prior - permission. Title to copyright in this software and any associated - documentation will at all times remain with copyright holders. - Files: etc/test/junit-noframes.xsl Copyright: 2001-2004 The Apache Software Foundation License: Apache-2.0 @@ -93,125 +41,10 @@ License: Apache-2.0 Comment: On Debian systems, the complete text of the Apache License version 2.0 is available in the file ‘/usr/share/common-licenses/Apache-2.0’. -Files: src/c/inteldeflater/IntelDeflater.c - src/java/net/sf/samtools/util/zip/IntelDeflater.java - src/java/net/sf/samtools/util/zip/ZStreamRef.java -Copyright: (c) 1996, 1996, 2009, 2010, Oracle and/or its affiliates. All rights reserved. -License: GPL-2 with Classpath exception - This code is free software; you can redistribute it and/or modify it - under the terms of the GNU General Public License version 2 only, as - published by the Free Software Foundation. Oracle designates this - particular file as subject to the "Classpath" exception as provided - by Oracle in the LICENSE file that accompanied this code. - . - This code is distributed in the hope that it will be useful, but WITHOUT - ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or - FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License - version 2 for more details (a copy is included in the LICENSE file that - accompanied this code). - . - You should have received a copy of the GNU General Public License version - 2 along with this work; if not, write to the Free Software Foundation, - Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. - . - Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA - or visit www.oracle.com if you need additional information or have any - questions. -Comment: - Comment on Classpath exception: here is quote from - http://spdx.org/licenses/GPL-2.0-with-classpath-exception - . - Linking this library statically or dynamically with other modules is making a - combined work based on this library. Thus, the terms and conditions of the GNU - General Public License cover the whole combination. - . - As a special exception, the copyright holders of this library give you - permission to link this library with independent modules to produce an - executable, regardless of the license terms of these independent modules, and - to copy and distribute the resulting executable under terms of your choice, - provided that you also meet, for each linked independent module, the terms and - conditions of the license of that module. An independent module is a module - which is not derived from or based on this library. If you modify this library, - you may extend this exception to your version of the library, but you are not - obligated to do so. If you do not wish to do so, delete this exception - statement from your version - . - . - Comment on the GPL-2: - . - On Debian systems, the complete text of the GNU General Public License - version 2 is available in the file ‘/usr/share/common-licenses/GPL-2’. - -Files: src/java/net/sf/samtools/seekablestream/SeekableFTPStream.java - src/java/net/sf/samtools/seekablestream/SeekableFTPStreamHelper.java - src/java/net/sf/samtools/seekablestream/SeekableFileStream.java - src/java/net/sf/samtools/util/ftp/FTPClient.java - src/java/net/sf/samtools/util/ftp/FTPReply.java - src/java/net/sf/samtools/util/ftp/FTPStream.java - src/java/net/sf/samtools/util/ftp/FTPUtils.java - src/java/org/broad/tribble/AbstractFeatureReader.java - src/java/org/broad/tribble/AsciiFeatureCodec.java - src/java/org/broad/tribble/CloseableTribbleIterator.java - src/java/org/broad/tribble/FeatureCodec.java - src/java/org/broad/tribble/FeatureReader.java - src/java/org/broad/tribble/index/AbstractIndex.java - src/java/org/broad/tribble/index/interval/Interval.java - src/java/org/broad/tribble/index/interval/IntervalIndexCreator.java - src/java/org/broad/tribble/index/interval/IntervalTree.java - src/java/org/broad/tribble/index/interval/IntervalTreeIndex.java - src/java/org/broad/tribble/index/linear/LinearIndex.java - src/java/org/broad/tribble/readers/AsciiLineReader.java - src/java/org/broad/tribble/readers/PositionalBufferedStream.java - src/java/org/broad/tribble/util/HTTPHelper.java - src/java/org/broad/tribble/util/URLHelper.java - src/tests/java/org/broad/tribble/index/interval/IntervalTreeTest.java - src/tests/java/org/broad/tribble/index/linear/LinearIndexTest.java -Comment: git grep 'lgpl-2.1' | cut -f 1 -d ':' - git grep 'lgpl-2.1' | cut -f 1 -d ':' | xargs grep -h Copyright -Copyright: * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved. - * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved. - * Copyright (c) 2007-2009 by The Broad Institute, Inc. and the Massachusetts Institute of Technology. - * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved. - * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved. - * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved. - * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved. - * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology. - * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology. - * Copyright (c) 2009-2010 by The Broad Institute, Inc. - * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology. - * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology. - * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology. - * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology. - * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology. - * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology. - * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology. - * Copyright (c) 2009-2010 by The Broad Institute, Inc. - * Copyright (c) 2007-2009 by The Broad Institute, Inc. and the Massachusetts Institute of Technology. - * Copyright (c) 2007-2009 by The Broad Institute, Inc. and the Massachusetts Institute of Technology. - * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved. - * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved. - * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology. - * Copyright (c) 2009-2010 by The Broad Institute, Inc. -License: LGPL-2.1 - Quoted from ‘/usr/share/common-licenses/LGPL-2.1’: - . - This library is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public - License as published by the Free Software Foundation; either - version 2.1 of the License, or (at your option) any later version. - . - This library is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - Lesser General Public License for more details. - . - You should have received a copy of the GNU Lesser General Public - License along with this library; if not, write to the Free Software - Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA - Files: debian/* Copyright: 2010 Shaun Jackman <[email protected]> 2013 Olivier Sallou <[email protected]> + 2015 Vincent Danjean <[email protected]> License: ISC Permission to use, copy, modify, and/or distribute this software for any purpose with or without fee is hereby granted, provided that the above diff --git a/debian/rules b/debian/rules index 161db85..e3b7747 100755 --- a/debian/rules +++ b/debian/rules @@ -15,23 +15,6 @@ override_dh_auto_configure: [ -d lib ] || mkdir lib # This empty directory is lost in the packages's Git clone. dh_auto_configure -# Adapted from http://wiki.debian.org/SandroTosi/Svn_get-orig-source -PACKAGE = picard-tools -SRC_VERSION = $(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p') -SRC_DIR = $(PACKAGE)-$(SRC_VERSION).orig -TARBALL = $(PACKAGE)_$(SRC_VERSION).orig.tar.xz -SVN_REPOS= http://svn.code.sf.net/p/picard/code -.PHONY: get-orig-source -get-orig-source: - rm -rf get-orig-source $(TARBALL) - mkdir get-orig-source - svn export $(SVN_REVISION) $(SVN_REPOS)/tags/$(SRC_VERSION) get-orig-source/$(SRC_DIR) - # Removing convenience binary jar files. - rm -r get-orig-source/$(SRC_DIR)/lib/* - tar cJf $(TARBALL) -C get-orig-source $(SRC_DIR) - rm -r get-orig-source - @echo " "$(TARBALL)" created; move it to the right destination to build the package" - override_dh_link: dh_link -p libsam-java usr/share/java/sam-$(SRC_VERSION).jar usr/share/java/sam.jar dh_link -p picard-tools usr/share/java/picard-$(SRC_VERSION).jar usr/share/java/picard.jar diff --git a/debian/watch b/debian/watch index f8083b5..a6e1393 100644 --- a/debian/watch +++ b/debian/watch @@ -1,2 +1,3 @@ version=3 -http://sf.net/picard/sam-(.+)\.jar +opts=dversionmangle=s/\+dfsg\.\d+$//,filenamemangle=s/.+\/v?(\d\S*)\.tar\.gz/picard-tools-$1.tar.gz/,uversionmangle=s/-rc/~rc/,repacksuffix=+dfsg.1 \ + https://github.com/broadinstitute/picard/releases .*/v?(\d\S*)\.tar\.gz -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/picard-tools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
