[med-svn] r594 - in trunk/packages/haploview/trunk: . debian
smoe-guest at alioth.debian.org
smoe-guest at alioth.debian.org
Thu Oct 4 22:09:52 UTC 2007
Author: smoe-guest
Date: 2007-10-04 22:09:52 +0000 (Thu, 04 Oct 2007)
New Revision: 594
Added:
trunk/packages/haploview/trunk/bla.txt
trunk/packages/haploview/trunk/debian/
trunk/packages/haploview/trunk/debian/README.Debian
trunk/packages/haploview/trunk/debian/changelog
trunk/packages/haploview/trunk/debian/compat
trunk/packages/haploview/trunk/debian/control
trunk/packages/haploview/trunk/debian/copyright
trunk/packages/haploview/trunk/debian/docs
trunk/packages/haploview/trunk/debian/haploview.dirs
trunk/packages/haploview/trunk/debian/haploview.doc-base.EX
trunk/packages/haploview/trunk/debian/manpage.1.ex
trunk/packages/haploview/trunk/debian/menu
trunk/packages/haploview/trunk/debian/rules
trunk/packages/haploview/trunk/debian/watch
trunk/packages/haploview/trunk/haploview.sh
Modified:
trunk/packages/haploview/trunk/build.xml
Log:
[svn-inject] Applying Debian modifications to trunk
Added: trunk/packages/haploview/trunk/bla.txt
===================================================================
--- trunk/packages/haploview/trunk/bla.txt (rev 0)
+++ trunk/packages/haploview/trunk/bla.txt 2007-10-04 22:09:52 UTC (rev 594)
@@ -0,0 +1,24 @@
+dpkg-buildpackage: source package is haploview
+dpkg-buildpackage: source version is 3.3-1
+dpkg-buildpackage: source changed by Steffen Moeller <moeller at unknown>
+dpkg-buildpackage: host architecture i386
+dpkg-buildpackage: source version without epoch 3.3-1
+test -x debian/rules
+test "`id -u`" = 0
+dh_clean
+cd . && /usr/bin/java -classpath /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/lib/kaffe/lib/tools.jar -Dant.home=/usr/share/ant org.apache.tools.ant.Main -Dcompile.debug=true -Dcompile.optimize=true clean
+Buildfile: build.xml
+
+init:
+
+clean:
+ [delete] Deleting directory /local/debian/home/moeller/debian/haploview/haploview-3.3/build
+
+BUILD SUCCESSFUL
+Total time: 0 seconds
+rm -f debian/stamp-ant-build
+dh_clean resources/jgrapht* Haploview.jar
+rm -rf build resources/jfreechart
+touch debian/files
+dpkg-source: building haploview using existing haploview_3.3.orig.tar.gz
+dpkg-source: building haploview in haploview_3.3-1.diff.gz
Modified: trunk/packages/haploview/trunk/build.xml
===================================================================
--- trunk/packages/haploview/trunk/build.xml 2007-10-04 22:09:28 UTC (rev 593)
+++ trunk/packages/haploview/trunk/build.xml 2007-10-04 22:09:52 UTC (rev 594)
@@ -14,11 +14,17 @@
<!-- Classpath -->
<path id="library.classpath">
+ <fileset dir="/usr/share/java/">
+ <include name="jgrapht.jar"/>
+ <include name="jfreechart.jar"/>
+ <include name="jcommon.jar"/>
+ </fileset>
+<!--
<fileset dir="resources/">
<include name="*.jar"/>
<include name="*.zip"/>
- <include name="jfreechart/*.jar"/>
- </fileset>
+ </fileset>
+-->
<fileset dir="docs/">
<include name="HaploHelp.jar"/>
</fileset>
@@ -74,9 +80,16 @@
<zipfileset src="resources/JimiProClasses.zip"/>
<zipfileset src="resources/jh.jar"/>
<zipfileset src="docs/HaploHelp.jar"/>
- <zipfileset src="resources/jgrapht-0.5.3.jar"/>
+<!--
+ <zipfileset src="resources/jgrapht-0.5.3.jar"/>
+-->
+ <zipfileset src="/usr/share/java/jgrapht.jar"/>
+<!--
<zipfileset src="resources/jfreechart/jfreechart-1.0.1.jar"/>
<zipfileset src="resources/jfreechart/jcommon-1.0.0.jar"/>
+-->
+ <zipfileset src="/usr/share/java/jfreechart.jar"/>
+ <zipfileset src="/usr/share/java/jcommon.jar"/>
</jar>
</target>
@@ -94,9 +107,14 @@
<zipfileset src="resources/JimiProClasses.zip"/>
<zipfileset src="resources/jh.jar"/>
<zipfileset src="docs/HaploHelp.jar"/>
- <zipfileset src="resources/jgrapht-0.5.3.jar"/>
+<!-- <zipfileset src="resources/jgrapht-0.5.3.jar"/> -->
+ <zipfileset src="/usr/share/java/jgrapht.jar"/>
+<!--
<zipfileset src="resources/jfreechart/jfreechart-1.0.1.jar"/>
<zipfileset src="resources/jfreechart/jcommon-1.0.0.jar"/>
+-->
+ <zipfileset src="/usr/share/java/jfreechart.jar"/>
+ <zipfileset src="/usr/share/java/jcommon.jar"/>
</jar>
</target>
Property changes on: trunk/packages/haploview/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/haploview/trunk/debian/README.Debian
===================================================================
--- trunk/packages/haploview/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/haploview/trunk/debian/README.Debian 2007-10-04 22:09:52 UTC (rev 594)
@@ -0,0 +1,10 @@
+haploview for Debian
+--------------------
+
+Quite frustrating for me but possibly stimulating for others,
+this package builds with kaffe but does not run without the Sun JDK.
+
+The watch file indicates the older 3.1.1 version rather than the 3.3
+since upstream omitted the second dot as a separator on sourceforge.net.
+
+ -- Steffen Moeller <steffen_moeller at gmx.de> Sun, 14 Jan 2007 15:28:10 +0100
Added: trunk/packages/haploview/trunk/debian/changelog
===================================================================
--- trunk/packages/haploview/trunk/debian/changelog (rev 0)
+++ trunk/packages/haploview/trunk/debian/changelog 2007-10-04 22:09:52 UTC (rev 594)
@@ -0,0 +1,6 @@
+haploview (3.3-1) unstable; urgency=low
+
+ * Initial release (Closes: #311421)
+
+ -- Steffen Moeller <moeller at unknown> Sun, 14 Jan 2007 15:28:10 +0100
+
Added: trunk/packages/haploview/trunk/debian/compat
===================================================================
--- trunk/packages/haploview/trunk/debian/compat (rev 0)
+++ trunk/packages/haploview/trunk/debian/compat 2007-10-04 22:09:52 UTC (rev 594)
@@ -0,0 +1 @@
+5
Added: trunk/packages/haploview/trunk/debian/control
===================================================================
--- trunk/packages/haploview/trunk/debian/control (rev 0)
+++ trunk/packages/haploview/trunk/debian/control 2007-10-04 22:09:52 UTC (rev 594)
@@ -0,0 +1,18 @@
+Source: haploview
+Section: contrib/science
+Priority: extra
+Maintainer: Steffen Moeller <steffen_moeller at gmx.de>
+Build-Depends-Indep: cdbs, ant, debhelper (>= 5), kaffe|java-compiler,libjfreechart-java,libjgrapht-java
+Standards-Version: 3.7.2
+
+Package: haploview
+Architecture: all
+Depends: java-virtual-machine, sun-java5-jre|java2-runtime,libjfreechart-java,libjgrapht-java, ${shlibs:Depends}, ${misc:Depends}
+Description: Analysis and visualization of LD and haplotype maps
+ This tools assists ín the analysis of the nucleotide
+ variation in a population. Such investigations are performed
+ to determine genes and genetic pathways that are associated
+ with diseases. This is an early stage in the quest for new drugs.
+ .
+ Homepage: http://www.broad.mit.edu/mpg/haploview/
+
Added: trunk/packages/haploview/trunk/debian/copyright
===================================================================
--- trunk/packages/haploview/trunk/debian/copyright (rev 0)
+++ trunk/packages/haploview/trunk/debian/copyright 2007-10-04 22:09:52 UTC (rev 594)
@@ -0,0 +1,19 @@
+This package was debianized by Steffen Moeller <steffen_moeller at gmx.de> on
+Sun, 14 Jan 2007 15:28:10 +0100.
+
+It was downloaded from www.sf.net/projects/haploview.
+
+Upstream Authors: Jeffrey Barrett, Julian Maller, David Bender <haploview at broad.mit.edu>
+
+Copyright: 2003-2006 Broad Institute of MIT and Harvard
+
+License:
+
+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.
+
+The Debian packaging is (C) 2007, Steffen Moeller <steffen_moeller at gmx.de> and
+is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
Added: trunk/packages/haploview/trunk/debian/docs
===================================================================
--- trunk/packages/haploview/trunk/debian/docs (rev 0)
+++ trunk/packages/haploview/trunk/debian/docs 2007-10-04 22:09:52 UTC (rev 594)
@@ -0,0 +1 @@
+README
Added: trunk/packages/haploview/trunk/debian/haploview.dirs
===================================================================
--- trunk/packages/haploview/trunk/debian/haploview.dirs (rev 0)
+++ trunk/packages/haploview/trunk/debian/haploview.dirs 2007-10-04 22:09:52 UTC (rev 594)
@@ -0,0 +1,2 @@
+usr/share/haploview
+usr/bin
Added: trunk/packages/haploview/trunk/debian/haploview.doc-base.EX
===================================================================
--- trunk/packages/haploview/trunk/debian/haploview.doc-base.EX (rev 0)
+++ trunk/packages/haploview/trunk/debian/haploview.doc-base.EX 2007-10-04 22:09:52 UTC (rev 594)
@@ -0,0 +1,22 @@
+Document: haploview
+Title: Debian haploview Manual
+Author: <insert document author here>
+Abstract: This manual describes what haploview is
+ and how it can be used to
+ manage online manuals on Debian systems.
+Section: unknown
+
+Format: debiandoc-sgml
+Files: /usr/share/doc/haploview/haploview.sgml.gz
+
+Format: postscript
+Files: /usr/share/doc/haploview/haploview.ps.gz
+
+Format: text
+Files: /usr/share/doc/haploview/haploview.text.gz
+
+Format: HTML
+Index: /usr/share/doc/haploview/html/index.html
+Files: /usr/share/doc/haploview/html/*.html
+
+
Added: trunk/packages/haploview/trunk/debian/manpage.1.ex
===================================================================
--- trunk/packages/haploview/trunk/debian/manpage.1.ex (rev 0)
+++ trunk/packages/haploview/trunk/debian/manpage.1.ex 2007-10-04 22:09:52 UTC (rev 594)
@@ -0,0 +1,59 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.TH HAPLOVIEW SECTION "January 14, 2007"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+haploview \- program to do something
+.SH SYNOPSIS
+.B haploview
+.RI [ options ] " files" ...
+.br
+.B bar
+.RI [ options ] " files" ...
+.SH DESCRIPTION
+This manual page documents briefly the
+.B haploview
+and
+.B bar
+commands.
+.PP
+.\" TeX users may be more comfortable with the \fB<whatever>\fP and
+.\" \fI<whatever>\fP escape sequences to invode bold face and italics,
+.\" respectively.
+\fBhaploview\fP is a program that...
+.SH OPTIONS
+These programs follow the usual GNU command line syntax, with long
+options starting with two dashes (`-').
+A summary of options is included below.
+For a complete description, see the Info files.
+.TP
+.B \-h, \-\-help
+Show summary of options.
+.TP
+.B \-v, \-\-version
+Show version of program.
+.SH SEE ALSO
+.BR bar (1),
+.BR baz (1).
+.br
+The programs are documented fully by
+.IR "The Rise and Fall of a Fooish Bar" ,
+available via the Info system.
+.SH AUTHOR
+haploview was written by <upstream author>.
+.PP
+This manual page was written by Steffen Moeller <moeller at unknown>,
+for the Debian project (but may be used by others).
Added: trunk/packages/haploview/trunk/debian/menu
===================================================================
--- trunk/packages/haploview/trunk/debian/menu (rev 0)
+++ trunk/packages/haploview/trunk/debian/menu 2007-10-04 22:09:52 UTC (rev 594)
@@ -0,0 +1,2 @@
+?package(haploview):needs="X11" section="Apps/Science"\
+ title="haploview" command="/usr/bin/haploview"
Added: trunk/packages/haploview/trunk/debian/rules
===================================================================
--- trunk/packages/haploview/trunk/debian/rules (rev 0)
+++ trunk/packages/haploview/trunk/debian/rules 2007-10-04 22:09:52 UTC (rev 594)
@@ -0,0 +1,29 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+#include /usr/share/cdbs/1/class/makefile.mk
+include /usr/share/cdbs/1/class/ant.mk
+
+JAVA_HOME=/usr/lib/kaffe
+JAVACMD=/usr/bin/java
+DEB_ANT_INSTALL_TARGET=haploview
+
+# Add here any variable or target overrides you need.
+
+DEB_JARS = jcommon,jgrapht,jfreechart
+
+DEB_INSTALL_EXAMPLES_haploview=$(shell ls examples/*)
+
+
+common-install-impl:: install/haploview
+#install/libjline-java-doc
+
+install/haploview:: DEB_FINALDIR=$(CURDIR)/debian/haploview
+install/haploview::
+ install -p -m 644 -D Haploview.jar $(DEB_FINALDIR)/usr/share/haploview/Haploview.jar
+ install -p -m 755 -D haploview.sh $(DEB_FINALDIR)/usr/bin/haploview
+
+clean::
+ dh_clean resources/jgrapht* Haploview.jar
+ rm -rf build resources/jfreechart
+ touch debian/files
Property changes on: trunk/packages/haploview/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/haploview/trunk/debian/watch
===================================================================
--- trunk/packages/haploview/trunk/debian/watch (rev 0)
+++ trunk/packages/haploview/trunk/debian/watch 2007-10-04 22:09:52 UTC (rev 594)
@@ -0,0 +1,12 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# See uscan(1) for format
+
+# Compulsory line, this is a version 3 file
+version=3
+
+# Uncomment to find new files on sourceforge, for debscripts >= 2.9
+http://sf.net/haploview/Haploview(.*)\.tar\.gz
+
+
Added: trunk/packages/haploview/trunk/haploview.sh
===================================================================
--- trunk/packages/haploview/trunk/haploview.sh (rev 0)
+++ trunk/packages/haploview/trunk/haploview.sh 2007-10-04 22:09:52 UTC (rev 594)
@@ -0,0 +1,2 @@
+#!/bin/sh
+export CLASSPATH=/usr/share/java/jgrapht.jar java -jar /usr/share/haploview/Haploview.jar
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