Author: tbooth-guest Date: 2011-12-14 13:06:03 +0000 (Wed, 14 Dec 2011) New Revision: 8950
Added: trunk/packages/libhmsbeagle/ trunk/packages/libhmsbeagle/trunk/ trunk/packages/libhmsbeagle/trunk/README.Debian trunk/packages/libhmsbeagle/trunk/README.source trunk/packages/libhmsbeagle/trunk/changelog trunk/packages/libhmsbeagle/trunk/compat trunk/packages/libhmsbeagle/trunk/control trunk/packages/libhmsbeagle/trunk/copyright trunk/packages/libhmsbeagle/trunk/docs trunk/packages/libhmsbeagle/trunk/get-orig-source trunk/packages/libhmsbeagle/trunk/libhmsbeagle-dev.dirs trunk/packages/libhmsbeagle/trunk/libhmsbeagle-dev.docs trunk/packages/libhmsbeagle/trunk/libhmsbeagle-dev.install trunk/packages/libhmsbeagle/trunk/libhmsbeagle-dev.manpages trunk/packages/libhmsbeagle/trunk/libhmsbeagle.doc-base.EX trunk/packages/libhmsbeagle/trunk/libhmsbeagle1.dirs trunk/packages/libhmsbeagle/trunk/libhmsbeagle1.install trunk/packages/libhmsbeagle/trunk/rules trunk/packages/libhmsbeagle/trunk/source/ trunk/packages/libhmsbeagle/trunk/source/format Log: Initial packaging for the "beagle" library. I've not tried to make it work with CUDA drivers yet nor have I tested the Java compatibility, but it does allow me to build the latest MrBayes. Added: trunk/packages/libhmsbeagle/trunk/README.Debian =================================================================== --- trunk/packages/libhmsbeagle/trunk/README.Debian (rev 0) +++ trunk/packages/libhmsbeagle/trunk/README.Debian 2011-12-14 13:06:03 UTC (rev 8950) @@ -0,0 +1,9 @@ +libhmsbeagle for Debian +----------------------- + +This is compiled from SVN. Used the internal name 'libhmsbeagle' to +differentiate from the other 'beagle'. +In the first instance I've not tested that the Java stuff works, only +that the package is sufficient to work with MrBayes. + + -- Tim Booth <[email protected]> Thu, 08 Dec 2011 17:05:04 +0000 Added: trunk/packages/libhmsbeagle/trunk/README.source =================================================================== --- trunk/packages/libhmsbeagle/trunk/README.source (rev 0) +++ trunk/packages/libhmsbeagle/trunk/README.source 2011-12-14 13:06:03 UTC (rev 8950) @@ -0,0 +1,17 @@ +libhmsbeagle for Debian +----------------------- + +<this file describes information about the source package, see Debian policy +manual section 4.14. You WILL either need to modify or delete this file> + +This package uses quilt to manage all modifications to the upstream +source. Changes are stored in the source package as diffs in +debian/patches and applied during the build. Please see: + + /usr/share/doc/quilt/README.source + +for more information on how to apply the patches, modify patches, or +remove a patch. + + + Added: trunk/packages/libhmsbeagle/trunk/changelog =================================================================== --- trunk/packages/libhmsbeagle/trunk/changelog (rev 0) +++ trunk/packages/libhmsbeagle/trunk/changelog 2011-12-14 13:06:03 UTC (rev 8950) @@ -0,0 +1,5 @@ +libhmsbeagle (0.1052-2) unstable; urgency=low + + * Initial build for PPA/experimental. + + -- Tim Booth <[email protected]> Mon, 12 Dec 2011 17:52:41 +0000 Added: trunk/packages/libhmsbeagle/trunk/compat =================================================================== --- trunk/packages/libhmsbeagle/trunk/compat (rev 0) +++ trunk/packages/libhmsbeagle/trunk/compat 2011-12-14 13:06:03 UTC (rev 8950) @@ -0,0 +1 @@ +7 Added: trunk/packages/libhmsbeagle/trunk/control =================================================================== --- trunk/packages/libhmsbeagle/trunk/control (rev 0) +++ trunk/packages/libhmsbeagle/trunk/control 2011-12-14 13:06:03 UTC (rev 8950) @@ -0,0 +1,43 @@ +Source: libhmsbeagle +Priority: extra +Maintainer: Tim Booth <[email protected]> +Build-Depends: quilt (>= 0.46-7~), debhelper (>= 7), autoconf (>= 2.65), automake (>= 1:1.11) , libtool, doxygen, openjdk-6-jdk +Standards-Version: 3.9.1 +Section: libs +Homepage: http://code.google.com/p/beagle-lib + +Package: libhmsbeagle-dev +Section: libdevel +Architecture: any +Depends: libhmsbeagle1 (= ${binary:Version}) +Description: High-performance lib for Bayesian and Maximum Likelihood phylogenetics + Development files needed to build against Beagel library + +Package: libhmsbeagle1 +Section: libs +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: High-performance lib for Bayesian and Maximum Likelihood phylogenetics + BEAGLE is a high-performance library that can perform the core calculations at + the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It + can make use of highly-parallel processors such as those in graphics cards + (GPUs) found in many PCs. + . + The project involves an open API and fast implementations of a library for + evaluating phylogenetic likelihoods (continuous time Markov processes) of + biomolecular sequence evolution. + . + The aim is to provide high performance evaluation 'services' to a wide range + of phylogenetic software, both Bayesian samplers and Maximum Likelihood + optimizers. This allows these packages to make use of implementations that + make use of optimized hardware such as graphics processing units. + . + A manuscript is now in press describing the BEAGLE API and library: + . + http://sysbio.oxfordjournals.org/content/early/2011/09/29/sysbio.syr100.abstract + . + The paper describing the algorithms used for calculating likelihoods of + sequences on trees using many core devices like graphics processing units + (GPUs) is available from: + . + http://tree.bio.ed.ac.uk/publications/390/ Added: trunk/packages/libhmsbeagle/trunk/copyright =================================================================== --- trunk/packages/libhmsbeagle/trunk/copyright (rev 0) +++ trunk/packages/libhmsbeagle/trunk/copyright 2011-12-14 13:06:03 UTC (rev 8950) @@ -0,0 +1,23 @@ +This work was packaged for Debian by: + + Tim Booth <[email protected]> on Thu, 08 Dec 2011 17:05:04 +0000 + +It was downloaded from http://code.google.com/p/beagle-lib/wiki/LinuxInstallInstructions + +Upstream Author(s): + + The BEAGLE Developer group (http://beagle-lib.googlecode.com) + +Copyright: + + Copyright (C) 2011 The BEAGLE Developer group + +License: + + GPL3 + +The Debian packaging is: + + Copyright (C) 2011 Tim Booth <[email protected]> + and is licensed under the GPL version 3, + see `/usr/share/common-licenses/GPL-3'. Added: trunk/packages/libhmsbeagle/trunk/docs =================================================================== --- trunk/packages/libhmsbeagle/trunk/docs (rev 0) +++ trunk/packages/libhmsbeagle/trunk/docs 2011-12-14 13:06:03 UTC (rev 8950) @@ -0,0 +1,2 @@ +NEWS +README Added: trunk/packages/libhmsbeagle/trunk/get-orig-source =================================================================== --- trunk/packages/libhmsbeagle/trunk/get-orig-source (rev 0) +++ trunk/packages/libhmsbeagle/trunk/get-orig-source 2011-12-14 13:06:03 UTC (rev 8950) @@ -0,0 +1,16 @@ +#!/bin/bash + +# Pulls from SVN and uses the "last changed revision" as the version number. + +set -e +set -u + +[ $0 = 'debian/get-orig-source' ] && pushd .. + +svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib +BVERS=`( cd beagle-lib ; svn info ) | grep '^Last Changed Rev: ' | sed 's/.*: //'` +tar --exclude-vcs -cvjf "libhmsbeagle_0.$BVERS.orig.tar.bz2" beagle-lib +rm -rf beagle-lib +echo "Checked out beagle-lib from SVN and compressed version 0.$BVERS" + +# popd || true Property changes on: trunk/packages/libhmsbeagle/trunk/get-orig-source ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/libhmsbeagle/trunk/libhmsbeagle-dev.dirs =================================================================== --- trunk/packages/libhmsbeagle/trunk/libhmsbeagle-dev.dirs (rev 0) +++ trunk/packages/libhmsbeagle/trunk/libhmsbeagle-dev.dirs 2011-12-14 13:06:03 UTC (rev 8950) @@ -0,0 +1,2 @@ +usr/lib +usr/include Added: trunk/packages/libhmsbeagle/trunk/libhmsbeagle-dev.docs =================================================================== --- trunk/packages/libhmsbeagle/trunk/libhmsbeagle-dev.docs (rev 0) +++ trunk/packages/libhmsbeagle/trunk/libhmsbeagle-dev.docs 2011-12-14 13:06:03 UTC (rev 8950) @@ -0,0 +1 @@ +doc/html Added: trunk/packages/libhmsbeagle/trunk/libhmsbeagle-dev.install =================================================================== --- trunk/packages/libhmsbeagle/trunk/libhmsbeagle-dev.install (rev 0) +++ trunk/packages/libhmsbeagle/trunk/libhmsbeagle-dev.install 2011-12-14 13:06:03 UTC (rev 8950) @@ -0,0 +1,5 @@ +usr/include/* +usr/lib/pkgconfig/* +usr/lib/*.la +usr/lib/lib*.so +usr/lib/jni/*.la Added: trunk/packages/libhmsbeagle/trunk/libhmsbeagle-dev.manpages =================================================================== --- trunk/packages/libhmsbeagle/trunk/libhmsbeagle-dev.manpages (rev 0) +++ trunk/packages/libhmsbeagle/trunk/libhmsbeagle-dev.manpages 2011-12-14 13:06:03 UTC (rev 8950) @@ -0,0 +1 @@ +doc/man/man3/* Added: trunk/packages/libhmsbeagle/trunk/libhmsbeagle.doc-base.EX =================================================================== --- trunk/packages/libhmsbeagle/trunk/libhmsbeagle.doc-base.EX (rev 0) +++ trunk/packages/libhmsbeagle/trunk/libhmsbeagle.doc-base.EX 2011-12-14 13:06:03 UTC (rev 8950) @@ -0,0 +1,20 @@ +Document: libhmsbeagle +Title: Debian libhmsbeagle Manual +Author: <insert document author here> +Abstract: This manual describes what libhmsbeagle is + and how it can be used to + manage online manuals on Debian systems. +Section: unknown + +Format: debiandoc-sgml +Files: /usr/share/doc/libhmsbeagle/libhmsbeagle.sgml.gz + +Format: postscript +Files: /usr/share/doc/libhmsbeagle/libhmsbeagle.ps.gz + +Format: text +Files: /usr/share/doc/libhmsbeagle/libhmsbeagle.text.gz + +Format: HTML +Index: /usr/share/doc/libhmsbeagle/html/index.html +Files: /usr/share/doc/libhmsbeagle/html/*.html Added: trunk/packages/libhmsbeagle/trunk/libhmsbeagle1.dirs =================================================================== --- trunk/packages/libhmsbeagle/trunk/libhmsbeagle1.dirs (rev 0) +++ trunk/packages/libhmsbeagle/trunk/libhmsbeagle1.dirs 2011-12-14 13:06:03 UTC (rev 8950) @@ -0,0 +1 @@ +usr/lib Added: trunk/packages/libhmsbeagle/trunk/libhmsbeagle1.install =================================================================== --- trunk/packages/libhmsbeagle/trunk/libhmsbeagle1.install (rev 0) +++ trunk/packages/libhmsbeagle/trunk/libhmsbeagle1.install 2011-12-14 13:06:03 UTC (rev 8950) @@ -0,0 +1,2 @@ +usr/lib/lib*.so.* +usr/lib/jni/*.so Added: trunk/packages/libhmsbeagle/trunk/rules =================================================================== --- trunk/packages/libhmsbeagle/trunk/rules (rev 0) +++ trunk/packages/libhmsbeagle/trunk/rules 2011-12-14 13:06:03 UTC (rev 8950) @@ -0,0 +1,34 @@ +#!/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 + +%: + dh --with quilt $@ + +override_dh_auto_configure: + ./autogen.sh + dh_auto_configure -- --enable-doxygen-man + +override_dh_auto_build: + $(MAKE) + $(MAKE) doxygen-doc + +override_dh_auto_install: + dh_auto_install + #Shunt jni .so to jni directory. + mkdir -p -m755 debian/tmp/usr/lib/jni + mv debian/tmp/usr/lib/*jni.* debian/tmp/usr/lib/jni + sed -i "s/libdir='\/usr\/lib'/libdir='\/usr\/lib\/jni'/" debian/tmp/usr/lib/jni/libhmsbeagle-jni.la + #dh_install doc/man /usr/share + #dh_install doc/html /usr/share/doc/libhmsbeagle1 + +override_dh_auto_clean: + $(MAKE) -f Makefile distclean || true + rm -rf doc .config configure Property changes on: trunk/packages/libhmsbeagle/trunk/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/libhmsbeagle/trunk/source/format =================================================================== --- trunk/packages/libhmsbeagle/trunk/source/format (rev 0) +++ trunk/packages/libhmsbeagle/trunk/source/format 2011-12-14 13:06:03 UTC (rev 8950) @@ -0,0 +1 @@ +3.0 (quilt) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
