[med-svn] [libpll] 02/02: Initial packaging
Andreas Tille
tille at debian.org
Tue Mar 14 14:41:23 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libpll.
commit a9a0d574326b3c914cc7f315de2d3ce3203e365e
Author: Andreas Tille <tille at debian.org>
Date: Tue Mar 14 15:39:44 2017 +0100
Initial packaging
---
debian/changelog | 5 ++
debian/clean | 10 ++++
debian/compat | 1 +
debian/control | 117 +++++++++++++++++++++++++++++++++++++++++++++++
debian/copyright | 26 +++++++++++
debian/rules | 25 ++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 7 +++
debian/watch | 3 ++
9 files changed, 195 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..26a7193
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+libpll (1.0.11-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Mon, 13 Mar 2017 15:54:20 +0100
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..9cbf496
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1,10 @@
+src/*.a
+src/*.la
+src/.dirstamp
+MPI/Makefile
+config.status
+Makefile
+config.h
+config.log
+libtool
+stamp-h1
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..f9f5470
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,117 @@
+Source: libpll
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 10),
+ d-shlibs
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libpll.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/libpll.git
+Homepage: http://www.libpll.org/
+
+Package: libpll-avx1
+Section: libs
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Phylogenetic Likelihood Library (AVX version)
+ PLL is a highly optimized, parallized software library to ease the
+ development of new software tools dealing with phylogenetic inference.
+ .
+ Among the functions included in PLL are parsing multiple sequence
+ alignments (MSA) from PHYLIP and FASTA files, reading Newick trees,
+ performing topological moves such as SPR and NNI, model optimization,
+ likelihood evaluation and partitioned analysis by assigning different
+ substitution models to each partition of the MSA. PLL fully implements
+ the GTR nucleotide substitution model for DNA data and a number of
+ models for aminoacid data.
+ .
+ It comes in three flavours — single-thread, POSIX Threads, and MPI.
+ Each version is optimized for the Streaming SIMD Extensions 3 (SSE3) and
+ Advanced Vector Extensions (AVX).
+
+Package: libpll-sse3-1
+Section: libs
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Phylogenetic Likelihood Library (SSE3 version)
+ PLL is a highly optimized, parallized software library to ease the
+ development of new software tools dealing with phylogenetic inference.
+ .
+ Among the functions included in PLL are parsing multiple sequence
+ alignments (MSA) from PHYLIP and FASTA files, reading Newick trees,
+ performing topological moves such as SPR and NNI, model optimization,
+ likelihood evaluation and partitioned analysis by assigning different
+ substitution models to each partition of the MSA. PLL fully implements
+ the GTR nucleotide substitution model for DNA data and a number of
+ models for aminoacid data.
+ .
+ It comes in three flavours — single-thread, POSIX Threads, and MPI.
+ Each version is optimized for the Streaming SIMD Extensions 3 (SSE3) and
+ Advanced Vector Extensions (AVX).
+
+Package: libpll-headers
+Section: libdevel
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Phylogenetic Likelihood Library (header files)
+ PLL is a highly optimized, parallized software library to ease the
+ development of new software tools dealing with phylogenetic inference.
+ .
+ Among the functions included in PLL are parsing multiple sequence
+ alignments (MSA) from PHYLIP and FASTA files, reading Newick trees,
+ performing topological moves such as SPR and NNI, model optimization,
+ likelihood evaluation and partitioned analysis by assigning different
+ substitution models to each partition of the MSA. PLL fully implements
+ the GTR nucleotide substitution model for DNA data and a number of
+ models for aminoacid data.
+ .
+ It comes in three flavours — single-thread, POSIX Threads, and MPI.
+ Each version is optimized for the Streaming SIMD Extensions 3 (SSE3) and
+ Advanced Vector Extensions (AVX).
+ .
+ This package contains the static library of the AVX version.
+
+Package: libpll-avx-dev
+Section: libdevel
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, libpll-headers, libpll-avx1 (= ${binary:Version})
+Description: Phylogenetic Likelihood Library (AVX version development files)
+ PLL is a highly optimized, parallized software library to ease the
+ development of new software tools dealing with phylogenetic inference.
+ .
+ Among the functions included in PLL are parsing multiple sequence
+ alignments (MSA) from PHYLIP and FASTA files, reading Newick trees,
+ performing topological moves such as SPR and NNI, model optimization,
+ likelihood evaluation and partitioned analysis by assigning different
+ substitution models to each partition of the MSA. PLL fully implements
+ the GTR nucleotide substitution model for DNA data and a number of
+ models for aminoacid data.
+ .
+ It comes in three flavours — single-thread, POSIX Threads, and MPI.
+ Each version is optimized for the Streaming SIMD Extensions 3 (SSE3) and
+ Advanced Vector Extensions (AVX).
+ .
+ This package contains the static library of the AVX version.
+
+Package: libpll-sse3-dev
+Section: libdevel
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, libpll-headers, libpll-sse3-1 (= ${binary:Version})
+Description: Phylogenetic Likelihood Library (SSE3 version development files)
+ PLL is a highly optimized, parallized software library to ease the
+ development of new software tools dealing with phylogenetic inference.
+ .
+ Among the functions included in PLL are parsing multiple sequence
+ alignments (MSA) from PHYLIP and FASTA files, reading Newick trees,
+ performing topological moves such as SPR and NNI, model optimization,
+ likelihood evaluation and partitioned analysis by assigning different
+ substitution models to each partition of the MSA. PLL fully implements
+ the GTR nucleotide substitution model for DNA data and a number of
+ models for aminoacid data.
+ .
+ It comes in three flavours — single-thread, POSIX Threads, and MPI.
+ Each version is optimized for the Streaming SIMD Extensions 3 (SSE3) and
+ Advanced Vector Extensions (AVX).
+ .
+ This package contains the static library of the SSE3 version.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..7f06277
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,26 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: PLL
+Source: http://www.libpll.org/
+
+Files: *
+Copyright: 2013-2015 Diego Darriba <Diego.Darriba at h-its.org>
+ Tomas Flouri <Tomas.Flouri at h-its.org>
+License: GPL-3+
+
+Files: debian/*
+Copyright: 2017 Andreas Tille <tille at debian.org>
+License: GPL-3+
+
+License: GPL-3+
+ This program 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, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This program 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.
+ .
+ On Debian systems you can find a copy of the GNU General Public License
+ version 3 at /usr/share/common-licenses/GPL-3.
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..7e7c768
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,25 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+BUILDTYPE := $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+
+%:
+ dh $@
+
+#override_dh_auto_configure:
+# dh_auto_configure -- --enable-generic
+
+override_dh_install:
+ dh_install
+ for lib in avx sse3 ; do \
+ d-shlibmove --commit \
+ --multiarch \
+ --devunversioned \
+ --exclude-la \
+ --movedev debian/tmp/usr/lib/$(BUILDTYPE)/libpll-$${lib}-pthreads.a usr/lib/$(BUILDTYPE) \
+ --movedev debian/tmp/usr/lib/$(BUILDTYPE)/libpll-$${lib}-mpi.a usr/lib/$(BUILDTYPE) \
+ debian/tmp/usr/lib/*/libpll-$${lib}.so ; \
+ mv debian/tmp/usr/lib/$(BUILDTYPE)/libpll-$${lib}-*.so debian/libpll-$${lib}-dev/usr/lib/$(BUILDTYPE) ; \
+ mv debian/tmp/usr/lib/$(BUILDTYPE)/libpll-$${lib}-*.so.* debian/libpll-$${lib}*1/usr/lib/$(BUILDTYPE) ; \
+ done
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..df9c8ea
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,7 @@
+Reference:
+ Author: Fernando Izquierdo-Carrasco and Nikolaos Alachiotis and Simon Berger and Tomas Flouri and Solon P. Pissis and Alexandros Stamatakis
+ Title: A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library
+ Journal: "Conference proceedings: Parallel and Distributed Processing Symposium Workshops"
+ Year: 2013
+ DOI: 10.1109/IPDPSW.2013.103
+ URL: http://ieeexplore.ieee.org/document/6650928/
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..4a74b4b
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+http://www.libpll.org/ Downloads/libpll-(\d[.\d]+)\.tar\.gz
--
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