[med-svn] [parsnp] 02/02: Initial debian/ packaging
Andreas Tille
tille at debian.org
Wed Apr 20 08:36:32 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository parsnp.
commit a7fa295d04baffdb0db6b4ec48527d3e6e487d18
Author: Andreas Tille <tille at debian.org>
Date: Wed Apr 20 10:35:50 2016 +0200
Initial debian/ packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 31 +++++++++++++++++++++++++
debian/copyright | 40 +++++++++++++++++++++++++++++++++
debian/patches/avoid_rpath.patch | 13 +++++++++++
debian/patches/fix_install_path.patch | 15 +++++++++++++
debian/patches/fix_libmuscle_path.patch | 40 +++++++++++++++++++++++++++++++++
debian/patches/fix_setup.py | 22 ++++++++++++++++++
debian/patches/series | 4 ++++
debian/rules | 22 ++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 8 +++++++
debian/watch | 4 ++++
13 files changed, 206 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..a4df062
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+parsnp (1.2+dfsg-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 15 Mar 2016 11:08:15 +0100
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..3b75b33
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,31 @@
+Source: parsnp
+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),
+ dh-autoreconf,
+ python-all-dev,
+ python-setuptools,
+ cython,
+ libmuscle-3.7-dev
+Standards-Version: 3.9.7
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/parsnp.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/parsnp.git
+Homepage: http://harvest.readthedocs.org/en/latest/content/parsnp.html
+X-Python-Version: >= 2.7
+
+Package: parsnp
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ fasttree,
+ phipack
+Description: rapid core genome multi-alignment
+ Parsnp was designed to align the core genome of hundreds to thousands of
+ bacterial genomes within a few minutes to few hours. Input can be both
+ draft assemblies and finished genomes, and output includes variant (SNP)
+ calls, core genome phylogeny and multi-alignments. Parsnp leverages
+ contextual information provided by multi-alignments surrounding SNP
+ sites for filtration/cleaning, in addition to existing tools for
+ recombination detection/filtration and phylogenetic reconstruction.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..17b24b9
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,40 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: ParSNP
+Upstream-Contact: Todd J Treangen <treangen at gmail.com>
+Source: https://github.com/marbl/parsnp/releases
+Files-Excluded: muscle
+ bin
+
+Files: *
+Copyright: 2014-2016, MarBL
+License: BSD-3-clause
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: BSD-3-clause
+
+License: BSD-3-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ * Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer.
+ .
+ * Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ .
+ * Neither the name of the {organization} nor the names of its
+ contributors may be used to endorse or promote products derived from
+ this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/debian/patches/avoid_rpath.patch b/debian/patches/avoid_rpath.patch
new file mode 100644
index 0000000..7802ade
--- /dev/null
+++ b/debian/patches/avoid_rpath.patch
@@ -0,0 +1,13 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 20 Apr 2016 10:31:32 +0200
+Description: There is no point in keeping rpath to a system library
+
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -1,5 +1,5 @@
+ parsnp_CXXFLAGS = -O3 -m64 -fopenmp -funroll-all-loops -fomit-frame-pointer -ftree-vectorize
+-parsnp_LDFLAGS = -lgomp -lstdc++ -lpthread -std=gnu++0x -Wl,-rpath,$(libmuscle)/lib -L$(libmuscle)/lib -lMUSCLE-3.7
++parsnp_LDFLAGS = -lgomp -lstdc++ -lpthread -std=gnu++0x -L$(libmuscle)/lib -lMUSCLE-3.7
+ bin_PROGRAMS = parsnp
+ parsnp_SOURCES = MuscleInterface.cpp MuscleInterface.h parsnp.cpp parsnp.hh LCB.cpp LCB.hh LCR.cpp LCR.hh TMum.cpp TMum.hh Converter.cpp Converter.hh ./ext/iniFile.cpp ./ext/iniFile.h
+ bindir = $(prefix)/bin
diff --git a/debian/patches/fix_install_path.patch b/debian/patches/fix_install_path.patch
new file mode 100644
index 0000000..e1fd511
--- /dev/null
+++ b/debian/patches/fix_install_path.patch
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 20 Apr 2016 10:31:32 +0200
+Description: Upstream per default installs into ../bin
+
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -2,6 +2,6 @@ parsnp_CXXFLAGS = -O3 -m64 -fopenmp -fun
+ parsnp_LDFLAGS = -lgomp -lstdc++ -lpthread -std=gnu++0x -Wl,-rpath,$(libmuscle)/lib -L$(libmuscle)/lib -lMUSCLE-3.7
+ bin_PROGRAMS = parsnp
+ parsnp_SOURCES = MuscleInterface.cpp MuscleInterface.h parsnp.cpp parsnp.hh LCB.cpp LCB.hh LCR.cpp LCR.hh TMum.cpp TMum.hh Converter.cpp Converter.hh ./ext/iniFile.cpp ./ext/iniFile.h
+-bindir = $(top_srcdir)/bin
+-libdir = $(top_srcdir)/lib
++bindir = $(prefix)/bin
++libdir = $(prefix)/lib
+
diff --git a/debian/patches/fix_libmuscle_path.patch b/debian/patches/fix_libmuscle_path.patch
new file mode 100644
index 0000000..9c0b37e
--- /dev/null
+++ b/debian/patches/fix_libmuscle_path.patch
@@ -0,0 +1,40 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 20 Apr 2016 10:31:32 +0200
+Description: We are using Debian packaged libMUSCLE
+ These includes are wrong anyway since this should be done via -I../muscle compiler option
+
+--- a/src/MuscleInterface.cpp
++++ b/src/MuscleInterface.cpp
+@@ -1,19 +1,19 @@
+ //Fork of libMUSCLE code from http://sourceforge.net/p/mauve/code/HEAD/tree/muscle/
+
+ #include "MuscleInterface.h"
+-#include "../muscle/libMUSCLE/muscle.h"
+-#include "../muscle/libMUSCLE/params.h"
+-#include "../muscle/libMUSCLE/seq.h"
+-#include "../muscle/libMUSCLE/seqvect.h"
+-#include "../muscle/libMUSCLE/msa.h"
+-#include "../muscle/libMUSCLE/tree.h"
+-#include "../muscle/libMUSCLE/clust.h"
+-#include "../muscle/libMUSCLE/profile.h"
+-#include "../muscle/libMUSCLE/distfunc.h"
+-#include "../muscle/libMUSCLE/clustsetdf.h"
+-#include "../muscle/libMUSCLE/textfile.h"
+-#include "../muscle/libMUSCLE/types.h"
+-#include "../muscle/libMUSCLE/threadstorage.h"
++#include "libMUSCLE/muscle.h"
++#include "libMUSCLE/params.h"
++#include "libMUSCLE/seq.h"
++#include "libMUSCLE/seqvect.h"
++#include "libMUSCLE/msa.h"
++#include "libMUSCLE/tree.h"
++#include "libMUSCLE/clust.h"
++#include "libMUSCLE/profile.h"
++#include "libMUSCLE/distfunc.h"
++#include "libMUSCLE/clustsetdf.h"
++#include "libMUSCLE/textfile.h"
++#include "libMUSCLE/types.h"
++#include "libMUSCLE/threadstorage.h"
+
+
+ namespace muscle {
diff --git a/debian/patches/fix_setup.py b/debian/patches/fix_setup.py
new file mode 100644
index 0000000..f9fa382
--- /dev/null
+++ b/debian/patches/fix_setup.py
@@ -0,0 +1,22 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 20 Apr 2016 10:31:32 +0200
+Description: NO idea for what purpose setup.py is used - in any case
+ it is seeking for a non-existing README file.
+
+--- a/setup.py
++++ b/setup.py
+@@ -17,11 +17,11 @@ setup(
+ license = "BSD",
+ keywords = "multialignment snps bionformatics",
+ url = "http://github.com/marbl/parsnp",
+- long_description=read('README'),
++ long_description=read('README.md'),
+ classifiers=[
+ "Development Status :: 1 - Release"
+ ],
+ scripts=['src/parsnp.py'],
+ # ext_modules = ext_modules,
+ cmdclass = {'build_ext': build_ext}
+- )
+\ No newline at end of file
++ )
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..6503e10
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,4 @@
+fix_libmuscle_path.patch
+fix_setup.py
+fix_install_path.patch
+avoid_rpath.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..61c9484
--- /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 $@ --with autoreconf
+
+override_dh_auto_configure:
+ dh_auto_configure -- --with-libmuscle=/usr/include/libMUSCLE-3.7
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..dafc34f
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,8 @@
+Reference:
+ Author: Todd J. Treangen and Brian D. Ondov and Sergey Koren and Adam M. Phillippy
+ Title: "Rapid Core-Genome Alignment and Visualization for Thousands of Intraspecific Microbial Genomes"
+ Journal: BioRxiv
+ Year: 2014
+ DOI: 10.1101/007351
+ URL: http://biorxiv.org/content/early/2014/10/20/007351
+ eprint: http://biorxiv.org/content/early/2014/10/20/007351.full.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..1a5c9ca
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+ https://github.com/marbl/parsnp/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
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