[med-svn] [beagle] 01/04: Remove embedded htsjdk
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Mon Apr 11 05:41:04 UTC 2016
This is an automated email from the git hooks/post-receive script.
bob.dybian-guest pushed a commit to branch master
in repository beagle.
commit 2d9f148d59a406c8c58e1225c797ff27900bc86a
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date: Sun Apr 10 15:19:32 2016 +0200
Remove embedded htsjdk
---
debian/changelog | 4 +--
debian/control | 2 +-
debian/copyright | 57 ++------------------------------
debian/patches/01_Update_to_htslib.patch | 27 +++++++++++++++
debian/patches/series | 1 +
debian/rules | 8 ++---
debian/watch | 3 +-
7 files changed, 39 insertions(+), 63 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index d5bbac9..ec2a568 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
-beagle (4.1~160222-8ef-1) unstable; urgency=low
+beagle (4.1~160222-8ef+dfsg-1) UNRELEASED; urgency=low
* Initial Debian Release. (Closes: #819301)
- -- Dylan Aïssi <bob.dybian at gmail.com> Sat, 26 Mar 2016 11:47:42 +0100
+ -- Dylan Aïssi <bob.dybian at gmail.com> Sun, 10 Apr 2016 09:55:48 +0200
diff --git a/debian/control b/debian/control
index c0eee15..205ca23 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,7 @@ Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Dylan Aïssi <bob.dybian at gmail.com>
Build-Depends: debhelper (>= 9), javahelper
-Build-Depends-Indep: default-jdk
+Build-Depends-Indep: default-jdk, libhtsjdk-java
Testsuite: autopkgtest
Standards-Version: 3.9.7
Vcs-Browser: https://anonscm.debian.org/git/debian-med/beagle.git
diff --git a/debian/copyright b/debian/copyright
index 8b9ef0b..e4a816c 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -2,6 +2,8 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: Beagle
Upstream-Contact: Brian L. Browning <browning at uw.edu>
Source: https://faculty.washington.edu/browning/beagle/beagle.html
+Comment: Remove embedded htsjdk (samtools)
+Files-Excluded: net
Files: *
Copyright: 2013-2016 Brian L. Browning
@@ -19,24 +21,6 @@ Files: beagleutil/IntIntervalTree.java
Copyright: 2013-2016 Brian L. Browning
License: Apache-2.0
-Files: net/sf/samtools/*
-Copyright: 2009 The Broad Institute (samtools)
-License: Expat
-
-Files: net/sf/samtools/Defaults.java
-Copyright: 2009 Tim Fennell and The Broad Institute (samtools)
-License: Expat
-
-Files: net/sf/samtools/util/HttpUtils.java
- net/sf/samtools/util/SeekableFileStream.java
- net/sf/samtools/util/SeekableHTTPStream.java
-Copyright: 2009 jrobinso and The Broad Institute (samtools)
-License: Expat
-
-Files: net/sf/samtools/util/SeekableStream.java
-Copyright: 2007-2009 The Broad Institute and Massachusetts Institute of Technology (samtools)
-License: GPL-2
-
Files: debian/*
Copyright: 2016 Dylan Aïssi <bob.dybian at gmail.com>
License: GPL-3+
@@ -79,40 +63,3 @@ License: Apache-2.0
On Debian systems, the full text of the Apache Software License version 2 can
be found in the file `/usr/share/common-licenses/Apache-2.0'.
-License: Expat
- 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.
-
-License: GPL-2
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License in version
- 2 of the license as published by the Free Software Foundation.
- .
- This package 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 for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this package; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
- .
- On Debian systems, the full text of the GNU General Public License
- version 2 can be found in `/usr/share/common-licenses/GPL-2'.
-
diff --git a/debian/patches/01_Update_to_htslib.patch b/debian/patches/01_Update_to_htslib.patch
new file mode 100644
index 0000000..8c0b98d
--- /dev/null
+++ b/debian/patches/01_Update_to_htslib.patch
@@ -0,0 +1,27 @@
+Author: Dylan Aïssi <bob.dybian at gmail.com>
+Description: Update references to htsjdk.
+Last-Update: 2016-04-09
+Forwarded: No
+
+--- a/blbutil/InputIt.java
++++ b/blbutil/InputIt.java
+@@ -28,7 +28,7 @@
+ import java.io.InputStreamReader;
+ import java.util.NoSuchElementException;
+ import java.util.zip.GZIPInputStream;
+-import net.sf.samtools.util.BlockCompressedInputStream;
++import htsjdk.samtools.util.BlockCompressedInputStream;
+
+ /**
+ * <p>Class {@code InputIt} is a buffered iterator whose {@code next()}
+--- a/blbutil/FileUtil.java
++++ b/blbutil/FileUtil.java
+@@ -32,7 +32,7 @@
+ import java.io.OutputStream;
+ import java.io.PrintWriter;
+ import java.util.zip.GZIPOutputStream;
+-import net.sf.samtools.util.BlockCompressedOutputStream;
++import htsjdk.samtools.util.BlockCompressedOutputStream;
+
+ /**
+ * Class {@code FileUtil} contains static methods for working with files.
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..91b927a
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+01_Update_to_htslib.patch
diff --git a/debian/rules b/debian/rules
index 8933b11..833cc9d 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,14 +1,14 @@
#!/usr/bin/make -f
-# -*- makefile -*-
-# debian/rules file for the Debian/GNU Linux beagle package
-# Copyright 2016 by Dylan Aïssi <bob.dybian at gmail.com>
export JAVA_HOME=/usr/lib/jvm/default-java
+export CLASSPATH=/usr/share/java/htsjdk.jar
%:
dh $@ --with javahelper
override_jh_build:
+ # This ugly thing below because jh_build search .java files in .pc folder so FTBFS...
+ rm -rf $(CURDIR)/.pc/
jh_build --javacopts="-source 1.8" --no-javadoc --main="main.Main" beagle.jar $(CURDIR)
# jh_build --javacopts="-source 1.8" --javadoc-opts="-source 1.8" --main="main.Main" beagle.jar $(CURDIR)
@@ -29,7 +29,7 @@ override_dh_link:
get-orig-source:
uscan --verbose --force-download --repack --compress xz
- # mv beagle_22Feb16.8ef.orig.tar.xz beagle_4.1~160222-8ef.orig.tar.xz
+ # mv beagle_22Feb16.8ef+dfsg.orig.tar.xz beagle_4.1~160222-8ef+dfsg.orig.tar.xz
# wget https://faculty.washington.edu/browning/beagle/beagle_4.1_09Feb16.pdf
# wget https://faculty.washington.edu/browning/beagle/release_notes
# wget https://faculty.washington.edu/browning/beagle/run.beagle.22Feb16.8ef.example
diff --git a/debian/watch b/debian/watch
index a5dbf6e..1fc1e7c 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,2 +1,3 @@
version=3
-https://faculty.washington.edu/browning/beagle/beagle.html beagle.(.*).src\.zip
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
+ https://faculty.washington.edu/browning/beagle/beagle.html beagle.(.*).src\.zip
--
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