[med-svn] [picard-tools] 01/05: Update package with new upstream web site

Vincent Danjean vdanjean at debian.org
Mon Sep 7 23:48:12 UTC 2015


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vdanjean pushed a commit to branch master
in repository picard-tools.

commit 023d7a17593fd19e8b9c1c8e72189ca50796b0b6
Author: Vincent Danjean <vdanjean at debian.org>
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 <vdanjean at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Shaun Jackman <sjackman at debian.org>,
            Charles Plessy <plessy at debian.org>,
-           Olivier Sallou <osallou at debian.org>
+           Olivier Sallou <osallou at debian.org>,
+           Vincent Danjean <vdanjean at debian.org>
 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 <sjackman at debian.org>
            2013 Olivier Sallou <osallou at debian.org>
+           2015 Vincent Danjean <vdanjean at debian.org>
 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

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