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 <[email protected]> +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 <[email protected]> +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 <[email protected]> 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 <[email protected]> + +# 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 <[email protected]>, +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 <[email protected]>, +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
