[med-svn] [iqtree] 02/02: Add initial Debian packaging (needs cmake help)
Andreas Tille
tille at debian.org
Mon Aug 31 08:57:32 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository iqtree.
commit b8146887ea59f3b2158955b121b150f2bfd74f3b
Author: Andreas Tille <tille at debian.org>
Date: Mon Aug 31 10:56:31 2015 +0200
Add initial Debian packaging (needs cmake help)
---
debian/changelog | 5 +++
debian/compat | 1 +
debian/control | 39 +++++++++++++++++++
debian/copyright | 35 +++++++++++++++++
debian/doc-base | 20 ++++++++++
debian/patches/series | 1 +
debian/patches/use_debian_packaged_libs.patch | 55 +++++++++++++++++++++++++++
debian/rules | 22 +++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++
debian/watch | 4 ++
11 files changed, 195 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..83a89b6
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+iqtree (1.3.8+dfsg-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Mon, 31 Aug 2015 09:22:55 +0200
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..200d710
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,39 @@
+Source: iqtree
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ cmake,
+ libeigen3-dev,
+ libsprng2-dev,
+ zlib1g-dev
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/iqtree.git
+Vcs-Git: git://anonscm.debian.org/debian-med/iqtree.git
+Homepage: http://www.cibiv.at/software/iqtree/
+
+Package: iqtree
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: efficient phylogenetic software by maximum likelihood
+ IQ-TREE is a very efficient maximum likelihood phylogenetic software
+ with following key features among others:
+ .
+ * A novel fast and effective stochastic algorithm to estimate maximum
+ likelihood trees. IQ-TREE outperforms both RAxML and PhyML in terms
+ of likelihood while requiring similar amount of computing time (see
+ Nguyen et al., 2015)
+ * An ultrafast bootstrap approximation to assess branch supports (see
+ Minh et al., 2013).
+ * A wide range of substitution models for binary, DNA, protein, codon,
+ and morphological alignments.
+ * Ultrafast model selection for all data types, 10 to 100 times faster
+ than jModelTest and ProtTest.
+ * Finding best partition scheme like PartitionFinder.
+ * Partitioned models with mixed data types for phylogenomic (multi-
+ gene) alignments, allowing for separate, proportional, or joint
+ branch lengths among genes.
+ * Supporting the phylogenetic likelihod library (PLL) (see Flouri et
+ al., 2014)
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..209f2b4
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,35 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: IQ-TREE
+Source: http://www.cibiv.at/software/iqtree/download/
+Files-Excluded: lib*/*
+ zlib-*
+ sprng
+ Eigen
+ .*
+ */.*
+
+Files: *
+Copyright: 2013-2015 <upstream>
+License: GPL-2+
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <maintainer at e.mail>
+License: GPL-2+
+
+License: GPL-2+
+ 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 2 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.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ .
+ On Debian systems you can find the full text of the GNU General Public
+ License version 2 or later at `/usr/share/common-licenses/GPL-2`.
diff --git a/debian/doc-base b/debian/doc-base
new file mode 100644
index 0000000..5e7e1d4
--- /dev/null
+++ b/debian/doc-base
@@ -0,0 +1,20 @@
+Document: <pkg>
+Title: <title for this doc>
+Author: <author of this doc>
+Abstract: <if you have no better clue the short and
+ long description from debian/control might fit here as well>
+Section: Science/{Biology,Medicine} # see /usr/share/doc/doc-base/doc-base.txt.gz "2.3.3. The `section' field"
+
+# pick one of the below options
+Format: Text
+Files: /usr/share/doc/<pkg>/<pkg>.txt.gz
+
+Format: html
+Index: /usr/share/doc/<pkg>/html/index.html
+Files: /usr/share/doc/<pkg>/html/*
+
+Format: pdf
+Files: /usr/share/doc/<pkg>/<pkg>.pdf.gz
+
+Format: postscript
+Files: /usr/share/doc/<pkg>/<pkg>.ps.gz
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..866f5f9
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+use_debian_packaged_libs.patch
diff --git a/debian/patches/use_debian_packaged_libs.patch b/debian/patches/use_debian_packaged_libs.patch
new file mode 100644
index 0000000..a629fa8
--- /dev/null
+++ b/debian/patches/use_debian_packaged_libs.patch
@@ -0,0 +1,55 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 31 Aug 2015 09:22:55 +0200
+Description: Use Debian packaged zlib, libsprng and libeigen
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -317,7 +317,6 @@ configure_file (
+ # add the binary tree to the search path for include files
+ # so that we will find iqtree_config.h
+ include_directories("${PROJECT_BINARY_DIR}")
+-include_directories("${PROJECT_BINARY_DIR}/zlib-1.2.7")
+
+
+ ##################################################################
+@@ -327,8 +326,6 @@ add_subdirectory(pllrepo/src)
+ add_subdirectory(ncl)
+ add_subdirectory(lbfgsb)
+ add_subdirectory(whtest)
+-add_subdirectory(sprng)
+-add_subdirectory(zlib-1.2.7)
+ add_subdirectory(vectorclass)
+ add_subdirectory(model)
+
+@@ -402,7 +399,7 @@ upperbounds.cpp
+ )
+
+ if (NOT IQTREE_FLAGS MATCHES "avx" AND NOT IQTREE_FLAGS MATCHES "fma")
+- set_target_properties(iqtree pll ncl lbfgsb whtest zlibstatic sprng vectorclass model PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
++ set_target_properties(iqtree pll ncl lbfgsb whtest vectorclass model PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
+ if (NOT BINARY32 AND NOT IQTREE_FLAGS MATCHES "novx")
+ set_target_properties(avxkernel pllavx PROPERTIES COMPILE_FLAGS "${AVX_FLAGS}")
+ endif()
+@@ -436,9 +433,9 @@ if (IQTREE_FLAGS MATCHES "omp")
+ endif()
+
+ if (BINARY32 OR IQTREE_FLAGS MATCHES "novx")
+- target_link_libraries(iqtree pll ncl lbfgsb whtest zlibstatic sprng vectorclass model ${PLATFORM_LIB} ${THREAD_LIB})
++ target_link_libraries(iqtree pll ncl lbfgsb whtest vectorclass model ${PLATFORM_LIB} ${THREAD_LIB})
+ else()
+- target_link_libraries(iqtree pll pllavx ncl lbfgsb whtest zlibstatic sprng vectorclass model avxkernel ${PLATFORM_LIB} ${THREAD_LIB})
++ target_link_libraries(iqtree pll pllavx ncl lbfgsb whtest vectorclass model avxkernel ${PLATFORM_LIB} ${THREAD_LIB})
+ endif()
+
+ ##################################################################
+--- a/phylotree.h
++++ b/phylotree.h
+@@ -22,7 +22,7 @@
+
+ //#define EIGEN_TUNE_FOR_CPU_CACHE_SIZE (512*256)
+ //#define EIGEN_TUNE_FOR_CPU_CACHE_SIZE (8*512*512)
+-#include "Eigen/Core"
++#include "eigen3/Eigen/Core"
+ #include "mtree.h"
+ #include "alignment.h"
+ #include "model/modelsubst.h"
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..7a8ee54
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# alternatively to manually set those variables, you can
+# include /usr/share/dpkg/default.mk
+# and use what is set there.
+
+%:
+ dh $@
+
+get-orig-source:
+ uscan --verbose --force-download --repack --compression xz
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..23110ca
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Lam Tung Nguyen and Heiko A. Schmidt and Arndt von Haeseler and and Bui Quang Minh
+ Title: "IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies"
+ Journal: Mol. Biol. Evol.
+ Year: 2015
+ Volume: 32
+ Number: 1
+ Pages: 268-274
+ DOI: 10.1093/molbev/msu300
+ PMID: 25371430
+ URL: http://mbe.oxfordjournals.org/content/32/1/268
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/31/15/2577
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..a4b913f
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="dversionmangle=s/\+dfsg\d*$//,repacksuffix=+dfsg" \
+ http://www.cibiv.at/software/iqtree/ download/iqtree-.*/iqtree-(\d[\d.]+)-Source\.tar\.gz
--
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