[med-svn] [phyutility] 02/02: initial commit

[Stephen Smith]

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blackrim-guest pushed a commit to branch master
in repository phyutility.

commit 3c67182c3bddb7dddd58fbb5022c870b631dc5ba
Author: blackrim-guest <blackrim at gmail.com>
Date:   Tue Mar 4 13:14:05 2014 -0500

    initial commit
---
 debian/bin/phyutility |  2 ++
 debian/changelog      |  5 +++++
 debian/compat         |  1 +
 debian/control        | 42 ++++++++++++++++++++++++++++++++++++++++++
 debian/copyright      | 30 ++++++++++++++++++++++++++++++
 debian/install        |  1 +
 debian/jlibs          |  1 +
 debian/rules          | 12 ++++++++++++
 debian/source/format  |  1 +
 debian/watch          |  3 +++
 10 files changed, 98 insertions(+)

diff --git a/debian/bin/phyutility b/debian/bin/phyutility
new file mode 100644
index 0000000..442f0a5
--- /dev/null
+++ b/debian/bin/phyutility
@@ -0,0 +1,2 @@
+#!/bin/sh
+java -Xmx2g -jar /usr/share/java/phyutility.jar $*
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..42d150f
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+phyutility (2.2.4-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #?????)
+
+ -- Andreas Tille <tille at debian.org>  Mon, 21 Feb 2011 08:17:38 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..45a4fb7
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+8
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..687dbe3
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,42 @@
+Source: phyutility
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 8),
+               javahelper,
+               openjdk-6-jdk,
+               ant,
+               libjebl2-java
+Standards-Version: 3.9.5
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/phyutility/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/phyutility/trunk
+Homepage: http://code.google.com/p/phyutility/
+
+Package: phyutility
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         ${java:Depends}
+Description: simple analyses or modifications on both phylogenetic trees and data matrices
+ Phyutility (fyoo-til-i-te) is a command line program that performs
+ simple analyses or modifications on both trees and data matrices.
+ .
+ Currently it performs the following functions (to suggest another
+ feature, submit an Issue and use the label Type-Enhancement) :
+ .
+ Trees
+  * rerooting
+  * pruning
+  * type conversion
+  * consensus
+  * leaf stability
+  * lineage movement
+  * tree support 
+ .
+ Data Matrices
+  * concatenate alignments
+  * genbank parsing
+  * trimming alignments
+  * search NCBI
+  * fetch NCBI
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..ac7c7d1
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,30 @@
+Format: http://dep.debian.net/deps/dep5/
+Upstream-Name: phyutility
+Upstream-Contact: Stephen Smith <blackrim at gmail.com>
+Source: http://code.google.com/p/phyutility/downloads
+
+Files: *
+Copyright: © 2007-2012 Stephen Smith <blackrim at gmail.com>
+License: GPL-3.0+
+
+Files: debian/*
+Copyright: 2012 Andreas Tille <tille at debian.org>
+License: GPL-3.0+
+
+License: GPL-3.0+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ 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 program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in
+ "/usr/share/common-licenses/GPL-3".
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..cba32dc
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+debian/bin/*	usr/bin
diff --git a/debian/jlibs b/debian/jlibs
new file mode 100644
index 0000000..16f637e
--- /dev/null
+++ b/debian/jlibs
@@ -0,0 +1 @@
+build/jar/*.jar
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..61cc498
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,12 @@
+#!/usr/bin/make -f
+
+JAVA_HOME=/usr/lib/jvm/default-java
+
+%:
+	dh $@ --with javahelper
+
+override_dh_auto_build:
+	ant compile && ant jar
+
+get-orig-source:
+	uscan --verbose --force-download
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..91224be
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+opts="dversionmangle=s/\./_/g" \
+   http://googlecode.debian.net/p/phyutility/phyutility_(.+)\.tar\.gz

-- 
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