[med-svn] r8418 - in trunk/packages/neobio/trunk/debian: . source usr usr/bin usr/share usr/share/man usr/share/man/man1
Christoph Gille
christophgil-guest at alioth.debian.org
Sat Nov 5 14:53:22 UTC 2011
Author: christophgil-guest
Date: 2011-11-05 14:53:22 +0000 (Sat, 05 Nov 2011)
New Revision: 8418
Added:
trunk/packages/neobio/trunk/debian/compat
trunk/packages/neobio/trunk/debian/control
trunk/packages/neobio/trunk/debian/control~
trunk/packages/neobio/trunk/debian/copyright
trunk/packages/neobio/trunk/debian/docs
trunk/packages/neobio/trunk/debian/menu.ex
trunk/packages/neobio/trunk/debian/neobio.1
trunk/packages/neobio/trunk/debian/neobio.default.ex
trunk/packages/neobio/trunk/debian/neobio.dirs
trunk/packages/neobio/trunk/debian/neobio.dirs~
trunk/packages/neobio/trunk/debian/neobio.doc-base.EX
trunk/packages/neobio/trunk/debian/neobio.install
trunk/packages/neobio/trunk/debian/neobio.install~
trunk/packages/neobio/trunk/debian/neobio.links
trunk/packages/neobio/trunk/debian/neobio.manpages
trunk/packages/neobio/trunk/debian/neobio.sh
trunk/packages/neobio/trunk/debian/rules
trunk/packages/neobio/trunk/debian/rules.einfach~
trunk/packages/neobio/trunk/debian/rules~
trunk/packages/neobio/trunk/debian/source/
trunk/packages/neobio/trunk/debian/source/format
trunk/packages/neobio/trunk/debian/usr/
trunk/packages/neobio/trunk/debian/usr/bin/
trunk/packages/neobio/trunk/debian/usr/bin/neobio
trunk/packages/neobio/trunk/debian/usr/share/
trunk/packages/neobio/trunk/debian/usr/share/man/
trunk/packages/neobio/trunk/debian/usr/share/man/man1/
trunk/packages/neobio/trunk/debian/usr/share/man/man1/neobio.1
trunk/packages/neobio/trunk/debian/watch.ex
Log:
Added: trunk/packages/neobio/trunk/debian/compat
===================================================================
--- trunk/packages/neobio/trunk/debian/compat (rev 0)
+++ trunk/packages/neobio/trunk/debian/compat 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1 @@
+7
Added: trunk/packages/neobio/trunk/debian/control
===================================================================
--- trunk/packages/neobio/trunk/debian/control (rev 0)
+++ trunk/packages/neobio/trunk/debian/control 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1,17 @@
+Source: neobio
+Package: neobio
+Version: 1
+Section: science
+Priority: extra
+Maintainer: Christoph Gille <christophgil at googlemail.com>
+Build-Depends: debhelper (>= 7.0.50~)
+Standards-Version: 3.8.4
+Homepage: http://neobio.sourceforge.net/
+Installed-Size: 100
+Architecture: all
+Depends: openjdk-6-jre | sun-java6-jre, java-wrappers
+Recommends: strap
+Enhances: strap
+Description: Library and graphical user interface for (pairwise) sequence alignments.
+ Implementation of the dynamic programming methods of Needleman & Wunsch (global alignment)
+ and Smith & Waterman (local alignment).
Added: trunk/packages/neobio/trunk/debian/control~
===================================================================
--- trunk/packages/neobio/trunk/debian/control~ (rev 0)
+++ trunk/packages/neobio/trunk/debian/control~ 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1,15 @@
+Source: neobio
+Section: unknown
+Priority: extra
+Maintainer: Christoph Gille <christophgil at googlemail.com>
+Build-Depends: debhelper (>= 7.0.50~)
+Standards-Version: 3.8.4
+Homepage: <insert the upstream URL, if relevant>
+#Vcs-Git: git://git.debian.org/collab-maint/neobio.git
+#Vcs-Browser: http://git.debian.org/?p=collab-maint/neobio.git;a=summary
+
+Package: neobio
+Architecture: all
+Depends: ${misc:Depends}
+Description: <insert up to 60 chars description>
+ <insert long description, indented with spaces>
Added: trunk/packages/neobio/trunk/debian/copyright
===================================================================
--- trunk/packages/neobio/trunk/debian/copyright (rev 0)
+++ trunk/packages/neobio/trunk/debian/copyright 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1,37 @@
+This work was packaged for Debian by:
+
+ Christoph Gille <christophgil at googlemail.com> on Sun, 30 Oct 2011 12:38:49 +0100
+
+It was downloaded from:
+
+ <url://example.com>
+
+Upstream Author(s):
+
+ <put author's name and email here>
+ <likewise for another author>
+
+Copyright:
+
+ <Copyright (C) YYYY Firstname Lastname>
+ <likewise for another author>
+
+License:
+
+ <Put the license of the package here indented by 4 spaces>
+
+The Debian packaging is:
+
+ Copyright (C) 2011 Christoph Gille <christophgil at googlemail.com>
+
+# Please chose a license for your packaging work. If the program you package
+# uses a mainstream license, using the same license is the safest choice.
+# Please avoid to pick license terms that are more restrictive than the
+# packaged work, as it may make Debian's contributions unacceptable upstream.
+# If you just want it to be GPL version 3, leave the following lines in.
+
+and is licensed under the GPL version 3,
+see "/usr/share/common-licenses/GPL-3".
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
Added: trunk/packages/neobio/trunk/debian/docs
===================================================================
--- trunk/packages/neobio/trunk/debian/docs (rev 0)
+++ trunk/packages/neobio/trunk/debian/docs 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1 @@
+license.txt
Added: trunk/packages/neobio/trunk/debian/menu.ex
===================================================================
--- trunk/packages/neobio/trunk/debian/menu.ex (rev 0)
+++ trunk/packages/neobio/trunk/debian/menu.ex 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1,2 @@
+?package(neobio):needs="X11|text|vc|wm" section="Applications/see-menu-manual"\
+ title="neobio" command="/usr/bin/neobio"
Added: trunk/packages/neobio/trunk/debian/neobio.1
===================================================================
--- trunk/packages/neobio/trunk/debian/neobio.1 (rev 0)
+++ trunk/packages/neobio/trunk/debian/neobio.1 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1,29 @@
+.TH NEOBIO 1 "October 30, 2011"
+
+.SH NAME
+
+neobio \- Pairwise Amino acid sequence and nucleotide sequence alignment in Java
+.SH SYNOPSIS
+.B neobio
+.br
+.SH DESCRIPTION
+
+A graphical user interface is opened. Two amino acid or nucleotide
+sequences are entered by the user. The program aligns them
+automatically.
+
+.SH OPTIONS
+none
+
+.SH SEE ALSO
+
+.BR clustalw (1)
+.BR mafft (1)
+.BR strap (1)
+
+
+.SH AUTHOR
+neobio was written by Sergio Anibal de Carvalho Junior.
+.PP
+This manual page was written by Christoph Gille <christophgil at googlemail.com>,
+for the Debian project and may be used by others.
Added: trunk/packages/neobio/trunk/debian/neobio.default.ex
===================================================================
--- trunk/packages/neobio/trunk/debian/neobio.default.ex (rev 0)
+++ trunk/packages/neobio/trunk/debian/neobio.default.ex 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1,10 @@
+# Defaults for neobio initscript
+# sourced by /etc/init.d/neobio
+# installed at /etc/default/neobio by the maintainer scripts
+
+#
+# This is a POSIX shell fragment
+#
+
+# Additional options that are passed to the Daemon.
+DAEMON_OPTS=""
Added: trunk/packages/neobio/trunk/debian/neobio.dirs
===================================================================
--- trunk/packages/neobio/trunk/debian/neobio.dirs (rev 0)
+++ trunk/packages/neobio/trunk/debian/neobio.dirs 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1,3 @@
+usr/share/java
+usr/bin
+usr/share/man/man1
Added: trunk/packages/neobio/trunk/debian/neobio.dirs~
===================================================================
--- trunk/packages/neobio/trunk/debian/neobio.dirs~ (rev 0)
+++ trunk/packages/neobio/trunk/debian/neobio.dirs~ 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1,2 @@
+usr/share/java
+usr/bin
Added: trunk/packages/neobio/trunk/debian/neobio.doc-base.EX
===================================================================
--- trunk/packages/neobio/trunk/debian/neobio.doc-base.EX (rev 0)
+++ trunk/packages/neobio/trunk/debian/neobio.doc-base.EX 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1,20 @@
+Document: neobio
+Title: Debian neobio Manual
+Author: <insert document author here>
+Abstract: This manual describes what neobio is
+ and how it can be used to
+ manage online manuals on Debian systems.
+Section: unknown
+
+Format: debiandoc-sgml
+Files: /usr/share/doc/neobio/neobio.sgml.gz
+
+Format: postscript
+Files: /usr/share/doc/neobio/neobio.ps.gz
+
+Format: text
+Files: /usr/share/doc/neobio/neobio.text.gz
+
+Format: HTML
+Index: /usr/share/doc/neobio/html/index.html
+Files: /usr/share/doc/neobio/html/*.html
Added: trunk/packages/neobio/trunk/debian/neobio.install
===================================================================
--- trunk/packages/neobio/trunk/debian/neobio.install (rev 0)
+++ trunk/packages/neobio/trunk/debian/neobio.install 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1,2 @@
+/usr/bin/
+/usr/share/java/neobio-1.jar
Added: trunk/packages/neobio/trunk/debian/neobio.install~
===================================================================
--- trunk/packages/neobio/trunk/debian/neobio.install~ (rev 0)
+++ trunk/packages/neobio/trunk/debian/neobio.install~ 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1 @@
+usr/bin/hallo
Added: trunk/packages/neobio/trunk/debian/neobio.links
===================================================================
--- trunk/packages/neobio/trunk/debian/neobio.links (rev 0)
+++ trunk/packages/neobio/trunk/debian/neobio.links 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1,2 @@
+/usr/share/java/neobio-1.jar /usr/share/java/neobio.jar
+
Added: trunk/packages/neobio/trunk/debian/neobio.manpages
===================================================================
--- trunk/packages/neobio/trunk/debian/neobio.manpages (rev 0)
+++ trunk/packages/neobio/trunk/debian/neobio.manpages 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1 @@
+debian/*1
Added: trunk/packages/neobio/trunk/debian/neobio.sh
===================================================================
--- trunk/packages/neobio/trunk/debian/neobio.sh (rev 0)
+++ trunk/packages/neobio/trunk/debian/neobio.sh 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1,5 @@
+#!/bin/sh
+. /usr/lib/java-wrappers/java-wrappers.sh
+find_java_runtime java6
+
+exec $JAVA_HOME/bin/java -jar /usr/share/java/neobio-1.jar $*
Property changes on: trunk/packages/neobio/trunk/debian/neobio.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/neobio/trunk/debian/rules
===================================================================
--- trunk/packages/neobio/trunk/debian/rules (rev 0)
+++ trunk/packages/neobio/trunk/debian/rules 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1,82 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+SRC_TMP=$(CURDIR)/SRC_TMP
+debtmp := $(CURDIR)/debian/tmp
+
+UVERSION=1
+VERSION=1
+get-orig-source:
+
+config.status:
+
+build: build-stamp
+
+build-indep: build-stamp
+
+
+build-stamp:
+ $(MAKE)
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp
+
+ # Add here commands to clean up after the build process.
+ $(MAKE) clean
+ rm -rf $(debtmp)
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_prep
+ dh_installdirs
+
+ # Add here commands to install the package into debian/neobio
+ mkdir -p $(debtmp)/usr/share/applications
+ mkdir -p $(debtmp)/usr/bin
+ mkdir -p $(debtmp)/usr/share/java
+ mkdir -p $(debtmp)/usr/lib/neobio
+ cp -a data $(debtmp)/usr/lib/neobio/data
+ mkdir -p $(debtmp)/usr/share/doc/neobio
+ cp -a doc $(debtmp)/usr/share/doc/neobio
+ cp -a debian/neobio.sh $(debtmp)/usr/bin/neobio
+ cp -a neobio-1.jar $(debtmp)/usr/share/java/
+
+# Build architecture-independent files here.
+binary-arch: build install
+# We have nothing to do by default.
+
+# Build architecture-dependent files here.
+binary-indep: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installexamples
+ dh_install
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_makeshlibs
+ dh_python2 --no-guessing-versions
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install
Property changes on: trunk/packages/neobio/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/neobio/trunk/debian/rules.einfach~
===================================================================
--- trunk/packages/neobio/trunk/debian/rules.einfach~ (rev 0)
+++ trunk/packages/neobio/trunk/debian/rules.einfach~ 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1,13 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# export DH_VERBOSE=1
+
+
+
+%:
+ echo xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+ mkdir -p debian/tmp/usr/bin/
+ cp -a debian/neobio.sh debian/tmp/usr/bin/neobio
+ dh $@
+# mkdir -p debian/usr/bin/
+# cp -a debian/neobio.sh debian/usr/bin/neobio
Added: trunk/packages/neobio/trunk/debian/rules~
===================================================================
--- trunk/packages/neobio/trunk/debian/rules~ (rev 0)
+++ trunk/packages/neobio/trunk/debian/rules~ 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1,21 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+# export DH_VERBOSE=1
+
+
+
+%:
+ echo xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+ mkdir -p debian/tmp/usr/bin/
+ ls -l debian
+ cp -a debian/neobio.sh debian/tmp/usr/bin/neobio
+ dh $@
+# mkdir -p debian/usr/bin/
+# cp -a debian/neobio.sh debian/usr/bin/neobio
Property changes on: trunk/packages/neobio/trunk/debian/rules~
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/neobio/trunk/debian/source/format
===================================================================
--- trunk/packages/neobio/trunk/debian/source/format (rev 0)
+++ trunk/packages/neobio/trunk/debian/source/format 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/neobio/trunk/debian/usr/bin/neobio
===================================================================
--- trunk/packages/neobio/trunk/debian/usr/bin/neobio (rev 0)
+++ trunk/packages/neobio/trunk/debian/usr/bin/neobio 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1,5 @@
+#!/bin/sh
+. /usr/lib/java-wrappers/java-wrappers.sh
+find_java_runtime java6
+
+exec $JAVA_HOME/bin/java -jar /usr/share/java/neobio-1.jar $*
Property changes on: trunk/packages/neobio/trunk/debian/usr/bin/neobio
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/neobio/trunk/debian/usr/share/man/man1/neobio.1
===================================================================
--- trunk/packages/neobio/trunk/debian/usr/share/man/man1/neobio.1 (rev 0)
+++ trunk/packages/neobio/trunk/debian/usr/share/man/man1/neobio.1 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1,29 @@
+.TH NEOBIO 1 "October 30, 2011"
+
+.SH NAME
+
+neobio \- Pairwise Amino acid sequence and nucleotide sequence alignment in Java
+.SH SYNOPSIS
+.B neobio
+.br
+.SH DESCRIPTION
+
+A graphical user interface is opened. Two amino acid or nucleotide
+sequences are entered by the user. The program aligns them
+automatically.
+
+.SH OPTIONS
+none
+
+.SH SEE ALSO
+
+.BR clustalw (1)
+.BR mafft (1)
+.BR strap (1)
+
+
+.SH AUTHOR
+neobio was written by Sergio Anibal de Carvalho Junior.
+.PP
+This manual page was written by Christoph Gille <christophgil at googlemail.com>,
+for the Debian project and may be used by others.
Added: trunk/packages/neobio/trunk/debian/watch.ex
===================================================================
--- trunk/packages/neobio/trunk/debian/watch.ex (rev 0)
+++ trunk/packages/neobio/trunk/debian/watch.ex 2011-11-05 14:53:22 UTC (rev 8418)
@@ -0,0 +1,23 @@
+# 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 examine a Webpage
+# <Webpage URL> <string match>
+#http://www.example.com/downloads.php neobio-(.*)\.tar\.gz
+
+# Uncomment to examine a Webserver directory
+#http://www.example.com/pub/neobio-(.*)\.tar\.gz
+
+# Uncommment to examine a FTP server
+#ftp://ftp.example.com/pub/neobio-(.*)\.tar\.gz debian uupdate
+
+# Uncomment to find new files on sourceforge, for devscripts >= 2.9
+# http://sf.net/neobio/neobio-(.*)\.tar\.gz
+
+# Uncomment to find new files on GooglePages
+# http://example.googlepages.com/foo.html neobio-(.*)\.tar\.gz
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