[Debian-med-packaging] [SCM] picard-tools branch, master, updated. upstream/1.22-1-g14cd30c
Shaun Jackman
sjackman at debian.org
Wed Jun 16 00:48:06 UTC 2010
The following commit has been merged in the master branch:
commit 14cd30c2796a90f5e207e8b1b00bb0690211c968
Author: Shaun Jackman <sjackman at debian.org>
Date: Tue Jun 15 17:45:28 2010 -0700
Initial release.
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..76841a9
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,7 @@
+The original source was packaged from the upstream subversion
+repository:
+svn co https://picard.svn.sourceforge.net/svnroot/picard
+
+Binary files in lib/* have been removed.
+
+ -- Shaun Jackman <sjackman at debian.org> 2010-06-15
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..2bb50db
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+picard-tools (1.22-1) UNRELEASED; urgency=low
+
+ * Initial release. Closes: #586015.
+
+ -- Shaun Jackman <sjackman at debian.org> Tue, 15 Jun 2010 10:41:09 -0700
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..7f8f011
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+7
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..264df95
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,19 @@
+Source: picard-tools
+Section: java
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Shaun Jackman <sjackman at debian.org>
+Build-Depends: ant, openjdk-6-jdk|java-compiler, debhelper (>= 7.0.50~),
+ testng
+Standards-Version: 3.8.4
+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
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Java library to manipulate SAM and BAM files
+ SAM (Sequence Alignment/Map) format is a generic format for storing
+ large nucleotide sequence alignments.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..f65387e
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,84 @@
+Format-Specification: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=135
+Name: Picard
+Maintainer: samtools-devel at lists.sourceforge.net
+Source: http://sourceforge.net/projects/picard/files/
+
+Copyright: 2009 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: debian/*
+Copyright: 2010 Shaun Jackman <sjackman 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
+ copyright notice and this permission notice appear in all copies.
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..b90eb97
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+dist/*.jar usr/share/java
diff --git a/debian/links b/debian/links
new file mode 100644
index 0000000..fe1b842
--- /dev/null
+++ b/debian/links
@@ -0,0 +1 @@
+usr/share/java/sam-1.22.jar usr/share/java/sam.jar
diff --git a/debian/patches/debian-changes-1.22-1 b/debian/patches/debian-changes-1.22-1
new file mode 100644
index 0000000..f7647e4
--- /dev/null
+++ b/debian/patches/debian-changes-1.22-1
@@ -0,0 +1,53 @@
+Description: Upstream changes introduced in version 1.22-1
+ This patch has been created by dpkg-source during the package build.
+ Here's the last changelog entry, hopefully it gives details on why
+ those changes were made:
+ .
+ picard-tools (1.22-1) UNRELEASED; urgency=low
+ .
+ * Initial release. Closes: #586015.
+ .
+ The person named in the Author field signed this changelog entry.
+Author: Shaun Jackman <sjackman at debian.org>
+Bug-Debian: http://bugs.debian.org/586015
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: <vendor|upstream|other>, <url of original patch>
+Bug: <url in upstream bugtracker>
+Bug-Debian: http://bugs.debian.org/<bugnumber>
+Forwarded: <no|not-needed|url proving that it has been forwarded>
+Reviewed-By: <name and email of someone who approved the patch>
+Last-Update: <YYYY-MM-DD>
+
+--- picard-tools-1.22.orig/build.xml
++++ picard-tools-1.22/build.xml
+@@ -23,7 +23,7 @@
+ ~ THE SOFTWARE.
+ -->
+
+-<project name="picard-public" basedir="." default="all">
++<project name="picard-public" basedir="." default="sam-jar">
+
+ <property name="src" value="src/java"/>
+ <property name="src.test" value="src/tests"/>
+@@ -62,6 +62,7 @@
+ <fileset dir="${lib}">
+ <include name="**/*.jar"/>
+ </fileset>
++ <pathelement path="/usr/share/java/testng.jar"/>
+ </path>
+ </target>
+
+@@ -92,7 +93,7 @@
+ sourcepath="" srcdir="${src}"
+ includes ="net/sf/samtools/**/*.*"
+ excludes = "net/sf/picard/**/*.*"
+- executable="${JAVA_HOME_1_5}/bin/javac"
++ executable="javac"
+ compiler="javac1.5" fork="true">
+ <!--<compilerarg value="-Xlint:all"/>-->
+ <!--<compilerarg value="-Xlint:unchecked"/>-->
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..0a0097e
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+debian-changes-1.22-1
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..9ae5268
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,6 @@
+#!/usr/bin/make -f
+
+export DH_OPTIONS
+
+%:
+ dh $@
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..f8083b5
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/picard/sam-(.+)\.jar
--
manipulate SAM and BAM files
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