[med-svn] r8950 - in trunk/packages: . libhmsbeagle libhmsbeagle/trunk libhmsbeagle/trunk/source
Timothy Booth
tbooth-guest at alioth.debian.org
Wed Dec 14 13:06:03 UTC 2011
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 <tbooth at ceh.ac.uk> 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 <tbooth at ceh.ac.uk> 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 <tbooth at ceh.ac.uk>
+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 <tbooth at ceh.ac.uk> 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 <tbooth at ceh.ac.uk>
+ 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)
More information about the debian-med-commit
mailing list