--- picard-tools-1.74.orig/debian/README.source +++ picard-tools-1.74/debian/README.source @@ -0,0 +1,6 @@ +The original source was packaged from the upstream subversion +repository: debian/rules get-orig-source + +Binary files in lib/* have been removed. + + -- Shaun Jackman 2010-06-15 --- picard-tools-1.74.orig/debian/control +++ picard-tools-1.74/debian/control @@ -0,0 +1,44 @@ +Source: picard-tools +Section: science +Priority: optional +Maintainer: Guillermo Carrasco +Build-Depends: ant, ant-optional, ant-contrib, ivy, openjdk-6-jdk|java-compiler, testng, libbcel-java, libsnappy-dev, subversion, + debhelper (>= 7.0.50~) +Standards-Version: 3.9.3 +Homepage: http://picard.sourceforge.net/ +Vcs-Git: git://git.debian.org/git/debian-med/picard-tools.git +Vcs-Browser: http://git.debian.org/?p=debian-med/picard-tools.git + +Package: libsam-java +Section: java +Architecture: all +Depends: ${misc:Depends} +Suggests: picard-tools +Description: Java library to manipulate SAM and BAM files + SAM (Sequence Alignment/Map) format is a generic format for storing + large nucleotide sequence alignments. + +Package: picard-tools +Architecture: all +Depends: openjdk-6-jre|java-runtime, ${misc:Depends}, + libsam-java (>= ${source:Version}), ${python:Depends} +Suggests: python, r-base-core +Description: Command line tools to manipulate SAM and BAM files + SAM (Sequence Alignment/Map) format is a generic format for storing + large nucleotide sequence alignments. Picard Tools includes these + utilities to manipulate SAM and BAM files: + BamToBfq IlluminaBasecallsToSam + BuildBamIndex MarkDuplicates + CalculateHsMetrics MeanQualityByCycle + CleanSam MergeBamAlignment + CollectAlignmentSummaryMetrics MergeSamFiles + CollectGcBiasMetrics NormalizeFasta + CollectInsertSizeMetrics QualityScoreDistribution + CollectRnaSeqMetrics ReplaceSamHeader + CompareSAMs RevertSam + CreateSequenceDictionary SamFormatConverter + ExtractIlluminaBarcodes SamToFastq + EstimateLibraryComplexity SortSam + FastqToSam ValidateSamFile + FixMateInformation ViewSam + --- picard-tools-1.74.orig/debian/rules +++ picard-tools-1.74/debian/rules @@ -0,0 +1,33 @@ +#!/usr/bin/make -f + +export DH_OPTIONS + +%: + dh $@ + +override_dh_auto_configure: + [ -d lib ] || mkdir lib + 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)-1.74~svn.orig +TARBALL = $(PACKAGE)_1.74~svn.orig.tar.bz2 +SVN_REPOS = http://picard.svn.sourceforge.net/svnroot/picard +.PHONY: get-orig-source +get-orig-source: + rm -rf get-orig-source $(TARBALL) + mkdir get-orig-source + svn export $(SVN_REVISION) $(SVN_REPOS)/tags/1.74 get-orig-source/$(SRC_DIR) + + # Removing convenience binary jar files. + rm -r get-orig-source/$(SRC_DIR)/lib/* + BZIP2='--best' 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 + --- picard-tools-1.74.orig/debian/compat +++ picard-tools-1.74/debian/compat @@ -0,0 +1 @@ +7 --- picard-tools-1.74.orig/debian/copyright +++ picard-tools-1.74/debian/copyright @@ -0,0 +1,117 @@ +Format: http://dep.debian.net/deps/dep5/ +Source: http://picard.svn.sourceforge.net/viewvc/picard/tags/1.55/ +Comment: Some source files are removed, see debian/rules. + +Files: * +Copyright: © 2009–2011 The Broad Institute +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: + . + 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. + +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: src/java/net/sf/samtools/util/SeekableStream.java +Copyright: 2007-2009 the Broad Institute/Massachusetts Institute of Technology +License: GPL-2 + This is copyright (2007-2009) by the Broad Institute/Massachusetts Institute + of Technology. It is licensed to You under the Gnu Public License, Version 2.0 + (the "License"); you may not use this file except in compliance with + the License. You may obtain a copy of the License at + . + http://www.opensource.org/licenses/gpl-2.0.php + . + 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. +Comment: 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: etc/test/junit-noframes.xsl +Copyright: 2001-2004 The Apache Software Foundation +License: Apache-2.0 + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + . + http://www.apache.org/licenses/LICENSE-2.0 + . + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. +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: debian/* +Copyright: 2010 Shaun Jackman +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 + copyright notice and this permission notice appear in all copies. --- picard-tools-1.74.orig/debian/changelog +++ picard-tools-1.74/debian/changelog @@ -0,0 +1,18 @@ +picard-tools (1.74-1ubuntu1) precise; urgency=low + + * Initial release + + -- Guillermo Carrasco Mon, 13 Aug 2012 10:37:59 +0000 + +picard-tools (1.74-1ubuntu1) precise; urgency=low + + * dh_install should create target dirs and install individual jars + + -- Guillermo Carrasco Tue, 14 Aug 2012 11:51:40 +0000 + +picard-tools (1.74-1ubuntu1) precise; urgency=low + + * Modifyed the build.xml file to copy the jar files to the /usr/share/java/picard directory + * Deleted the file package.install + + -- Guillermo Carrasco Tue, 14 Aug 2012 12:53:06 +0000 --- picard-tools-1.74.orig/debian/install +++ picard-tools-1.74/debian/install @@ -0,0 +1 @@ +dist/*.jar /usr/share/java/picard