[med-svn] r1572 - in trunk/packages: . treeview treeview/trunk treeview/trunk/debian
tille at alioth.debian.org
tille at alioth.debian.org
Thu Mar 13 09:31:36 UTC 2008
Author: tille
Date: 2008-03-13 09:31:35 +0000 (Thu, 13 Mar 2008)
New Revision: 1572
Added:
trunk/packages/treeview/
trunk/packages/treeview/trunk/
trunk/packages/treeview/trunk/README
trunk/packages/treeview/trunk/debian/
trunk/packages/treeview/trunk/debian/README
trunk/packages/treeview/trunk/debian/README.Debian
trunk/packages/treeview/trunk/debian/changelog
trunk/packages/treeview/trunk/debian/compat
trunk/packages/treeview/trunk/debian/control
trunk/packages/treeview/trunk/debian/copyright
trunk/packages/treeview/trunk/debian/dirs
trunk/packages/treeview/trunk/debian/docs
trunk/packages/treeview/trunk/debian/menu
trunk/packages/treeview/trunk/debian/rules
trunk/packages/treeview/trunk/debian/treeview
trunk/packages/treeview/trunk/debian/treeview.sgml
Log:
Moved Steffen M?\195?\182llers work which was stalled to svn to keep track of previous work.
Added: trunk/packages/treeview/trunk/README
===================================================================
--- trunk/packages/treeview/trunk/README (rev 0)
+++ trunk/packages/treeview/trunk/README 2008-03-13 09:31:35 UTC (rev 1572)
@@ -0,0 +1,3 @@
+Work on this project was started by Steffen Möller but has stalled.
+Feel free to take it over.
+
Added: trunk/packages/treeview/trunk/debian/README
===================================================================
--- trunk/packages/treeview/trunk/debian/README (rev 0)
+++ trunk/packages/treeview/trunk/debian/README 2008-03-13 09:31:35 UTC (rev 1572)
@@ -0,0 +1,54 @@
+########################################################################
+# Treeview README file
+#
+# CONTENTS:
+#
+# 1) Description of files
+# 2) Cluster-3.0-OSX Integration
+#
+########################################################################
+
+1) Description of files:
+
+APPLET: TreeView-X.X.X-applet.tar.gz
+ working sample applet distribution - needs documentation!
+
+UNIX: TreeView-X.X.X-bin.tar.gz
+ distribution for unix/linux/etc
+
+WINDOWS: TreeView-X.X.X-win.zip
+ similar to .tar.gz, but easier to unpack on windows
+ also includes setup.exe, an installer written by Michiel Jan Laurens de Hoon
+
+SOURCE: TreeView-X.X.X-src.tar.gz
+ source distribution
+
+MAC OS X: TreeView-X.X.X-osx.dmg
+ distribution for mac os x
+
+Mac OS 9: Instructions for Mac OS9:
+
+Unfortunately, i no longer have access to an OS9 machine, and can no longer easily build a new distro.
+Here's what you need to do in order to get the latest treeview running:
+
+1) download and expand the TreeView-1.0.1-os9.sit file
+2) download and expand the latest TreeView-X.X.X-bin.tar.gz file
+3) copy over the TreeView.jar file to the 1.0.1-os9 folder, replacing the original.
+
+MANUAL: JTVUserManual-X.X.X.pdf
+ manual in pdf format, if updated since the last one
+ also available on the website, with the html version.
+
+########################################################################
+
+2) Cluster-3.0-OSX-Integration
+
+
+The following is a brief description of how to get the "Launch Treeview" button of cluster 3.0 (see http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm) to work nicely on Mac OSX.
+
+1) download the TreeView-X.X.X-bin.tar.gz file. This should unpack to make a TreeView-X.X.X-bin folder. Be sure not to get the TreeView-X.X.X-osx.dmg file by mistake.
+2) Rename the TreeView-X.X.X-bin folder to TreeView
+3) Move the TreeView folder to the Applications folder in the finder
+
+Double-clicking "Cluster" in the Applications folder, and then clicking the java treeview button should now work
+
Added: trunk/packages/treeview/trunk/debian/README.Debian
===================================================================
--- trunk/packages/treeview/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/treeview/trunk/debian/README.Debian 2008-03-13 09:31:35 UTC (rev 1572)
@@ -0,0 +1,6 @@
+treeview for Debian
+-------------------
+
+I need help with the correct specification of the dependency to non-free Java 1.4.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>, Wed, 7 Apr 2004 22:02:54 +0200
Added: trunk/packages/treeview/trunk/debian/changelog
===================================================================
--- trunk/packages/treeview/trunk/debian/changelog (rev 0)
+++ trunk/packages/treeview/trunk/debian/changelog 2008-03-13 09:31:35 UTC (rev 1572)
@@ -0,0 +1,27 @@
+treeview (1.0.10-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Thu, 6 Jan 2005 02:14:07 +0200
+
+
+treeview (1.0.5-0.3) unstable; urgency=low
+
+ * lintian clean (Closes: #243771).
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Wed, 14 Apr 2004 23:02:54 +0200
+
+treeview (1.0.5-0.2) unstable; urgency=low
+
+ * Added little man page.
+ * Moved to contrib because of dependency to non-free Java.
+ * Added build-dependency.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Wed, 8 Apr 2004 12:02:54 +0200
+
+treeview (1.0.5-0.1) unstable; urgency=low
+
+ * Initial Release.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Wed, 7 Apr 2004 22:02:54 +0200
+
Added: trunk/packages/treeview/trunk/debian/compat
===================================================================
--- trunk/packages/treeview/trunk/debian/compat (rev 0)
+++ trunk/packages/treeview/trunk/debian/compat 2008-03-13 09:31:35 UTC (rev 1572)
@@ -0,0 +1 @@
+4
Added: trunk/packages/treeview/trunk/debian/control
===================================================================
--- trunk/packages/treeview/trunk/debian/control (rev 0)
+++ trunk/packages/treeview/trunk/debian/control 2008-03-13 09:31:35 UTC (rev 1572)
@@ -0,0 +1,21 @@
+Source: treeview
+Section: contrib/science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at pzr.uni-rostock.de>
+Build-Depends: debhelper (>= 4.0.0), ant, java2-compiler
+Standards-Version: 3.6.0
+
+Package: treeview
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, java2-runtime
+Recommends: cluster3
+Suggests: mapletree, smile
+Description: [Biology] Java re-implementation of Michael Eisen's TreeView
+ TreeView creates a matrix-like display of expression data, known as
+ Eisen clustering. The original implementation was a Windows program
+ named TreeView by Michael Eisen. This TreeView package, sometimes also
+ referred to as jTreeView, was rewritten in Java under a free license,
+ the original implementation also comes with the source code, but controls
+ commercial distribution. And it did not run on Unix.
+ .
+ Homepage: http://jtreeview.sourceforge.net
Added: trunk/packages/treeview/trunk/debian/copyright
===================================================================
--- trunk/packages/treeview/trunk/debian/copyright (rev 0)
+++ trunk/packages/treeview/trunk/debian/copyright 2008-03-13 09:31:35 UTC (rev 1572)
@@ -0,0 +1,26 @@
+This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
+Wed, 7 Apr 2004 22:02:54 +0200.
+
+It was downloaded from http://treeview.sourceforge.net
+
+Upstream Author: Alok Saldanha <alok at caltech.edu>
+
+Copyright:
+
+ This package 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; version 2 dated June, 1991.
+
+ 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., 59 Temple Place - Suite 330, Boston, MA
+ 02111-1307, USA.
+
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL'.
+
Added: trunk/packages/treeview/trunk/debian/dirs
===================================================================
--- trunk/packages/treeview/trunk/debian/dirs (rev 0)
+++ trunk/packages/treeview/trunk/debian/dirs 2008-03-13 09:31:35 UTC (rev 1572)
@@ -0,0 +1,3 @@
+usr/bin
+usr/share/treeview
+usr/share/doc/treeview
Added: trunk/packages/treeview/trunk/debian/docs
===================================================================
--- trunk/packages/treeview/trunk/debian/docs (rev 0)
+++ trunk/packages/treeview/trunk/debian/docs 2008-03-13 09:31:35 UTC (rev 1572)
@@ -0,0 +1 @@
+debian/README
Added: trunk/packages/treeview/trunk/debian/menu
===================================================================
--- trunk/packages/treeview/trunk/debian/menu (rev 0)
+++ trunk/packages/treeview/trunk/debian/menu 2008-03-13 09:31:35 UTC (rev 1572)
@@ -0,0 +1 @@
+?package(treeview):needs="X11" section="Apps/Science" title="treeview" command="/usr/bin/treeview"
Added: trunk/packages/treeview/trunk/debian/rules
===================================================================
--- trunk/packages/treeview/trunk/debian/rules (rev 0)
+++ trunk/packages/treeview/trunk/debian/rules 2008-03-13 09:31:35 UTC (rev 1572)
@@ -0,0 +1,94 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# GNU copyright 1997 to 1999 by Joey Hess.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+
+
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
+ INSTALL_PROGRAM += -s
+endif
+
+configure: configure-stamp
+configure-stamp:
+ dh_testdir
+ # Add here commands to configure the package.
+
+ touch configure-stamp
+
+
+build: build-stamp
+
+build-stamp: configure-stamp
+ dh_testdir
+
+ # Add here commands to compile the package.
+ ant jar
+ #/usr/bin/docbook-to-man debian/treeview.sgml > treeview.1
+
+ touch build-stamp
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp configure-stamp
+
+ # Add here commands to clean up after the build process.
+ ant clean
+
+ find . -type d -name CVS | xargs --no-run-if-empty rm -r
+
+ dh_clean treeview.1
+
+treeview.1: debian/treeview.sgml
+ docbook-to-man $< > $@
+
+install: build treeview.1
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+ # Add here commands to install the package into debian/treeview.
+ mkdir -p $(CURDIR)/debian/treeview/usr/share/treeview/lib || true
+ cp TreeView.jar $(CURDIR)/debian/treeview/usr/share/treeview
+ cp debian/treeview $(CURDIR)/debian/treeview/usr/bin
+ chmod 755 $(CURDIR)/debian/treeview/usr/bin/treeview
+ cp lib/*.jar $(CURDIR)/debian/treeview/usr/share/treeview/lib
+
+
+# Build architecture-independent files here.
+binary-indep: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs doc/*
+ dh_installmenu
+ dh_installman treeview.1
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+# Build architecture-dependent files here.
+binary-arch: build install
+# We have nothing to do by default.
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure
Added: trunk/packages/treeview/trunk/debian/treeview
===================================================================
--- trunk/packages/treeview/trunk/debian/treeview (rev 0)
+++ trunk/packages/treeview/trunk/debian/treeview 2008-03-13 09:31:35 UTC (rev 1572)
@@ -0,0 +1,17 @@
+#!/bin/sh
+
+if [ -z $JAVA_HOME ]; then
+ java=java
+else
+ java=$JAVA_HOME/bin/java
+fi
+
+if [ -x /usr/share/mapletree ]; then
+ if [ -r /usr/share/treeview/TreeView.jar ]; then
+ cd /usr/share/treeview && $java -jar TreeView.jar
+ else
+ echo "Could not find /usr/share/treeview/TreeView.jar"
+ fi
+else
+ echo "Could not find /usr/share/treeview directory."
+fi
Added: trunk/packages/treeview/trunk/debian/treeview.sgml
===================================================================
--- trunk/packages/treeview/trunk/debian/treeview.sgml (rev 0)
+++ trunk/packages/treeview/trunk/debian/treeview.sgml 2008-03-13 09:31:35 UTC (rev 1572)
@@ -0,0 +1,118 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+ page: `docbook-to-man manpage.sgml > manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>FIRSTNAME</firstname>">
+ <!ENTITY dhsurname "<surname>SURNAME</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>April 7, 2004</date>">
+ <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+ allowed: see man(7), man(1). -->
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>TREEVIEW</refentrytitle>">
+ <!ENTITY dhpackage "treeview">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>Presentation of Eisen-clustering</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+
+ <para>TreeView is the Java-based Linux variant of the well-known Windows program of Michael Eisen for the display of clusterings of DNA microarray expression data.</para>
+
+ <para>This manual page was written for the &debian; distribution
+ because the original program does not have a manual page.
+ Instead, it has documentation in the &gnu;
+ <application>Info</application> format; see below.</para>
+
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+
+ <para>cluster3 (1), mapletree (1)</para>
+ <para>http://jtreeview.sourceforge.net</para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+
+ <para>This manual page was written by &dhusername; &dhemail; for
+ the &debian; system (but may be used by others). Permission is
+ granted to copy, distribute and/or modify this document under
+ the terms of the &gnu; General Public License, Version 2 any
+ later version published by the Free Software Foundation.
+ </para>
+ <para>
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+ </para>
+
+ </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
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