This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository libsmithwaterman.
commit 889aa4a4297a750abc24d44d352ce4cd73b06d6f Author: Andreas Tille <[email protected]> Date: Wed Jun 22 13:45:26 2016 +0200 Initial packaging until I'm struck with build problems --- debian/changelog | 5 ++ debian/compat | 1 + debian/control | 18 +++++ debian/copyright | 11 +++ debian/get-orig-source | 25 +++++++ debian/patches/autoconf.patch | 151 ++++++++++++++++++++++++++++++++++++++++++ debian/patches/series | 1 + debian/rules | 26 ++++++++ debian/source/format | 1 + debian/upstream/metadata | 12 ++++ debian/watch | 2 + 11 files changed, 253 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..7b47830 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +libsmithwaterman (0.0+20151117-1) UNRELEASED; urgency=medium + + * Initial release (Closes: #<bug>) + + -- DMPT <[email protected]> Wed, 22 Jun 2016 11:50:46 +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..59cca5e --- /dev/null +++ b/debian/control @@ -0,0 +1,18 @@ +Source: libsmithwaterman +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 9), + dh-autoreconf +Standards-Version: 3.9.8 +Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libsmithwaterman.git +Vcs-Git: https://anonscm.debian.org/git/debian-med/libsmithwaterman.git +Homepage: https://github.com/ekg/smithwaterman + +Package: libsmithwaterman +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: smith-waterman-gotoh alignment algorithm + This library is packaged as a precondition for libvcflib. There was no + better description found on its homepage. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..552ad2a --- /dev/null +++ b/debian/copyright @@ -0,0 +1,11 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: <pkg> +Source: <path_to_download> + +Files: * +Copyright: © 20xx-20yy <upstream> +License: <license> + +Files: debian/* +Copyright: © 2016 maintainername <[email protected]> +License: <license> diff --git a/debian/get-orig-source b/debian/get-orig-source new file mode 100755 index 0000000..6759e4f --- /dev/null +++ b/debian/get-orig-source @@ -0,0 +1,25 @@ +#!/bin/sh -e + +COMPRESS=xz + +NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` +ORIGNAME=`echo $NAME | sed 's/^lib//'` +MVERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/^\([0-9\.]\+\)[+~][-0-9]\+$/\1/'` + +mkdir -p ../tarballs +cd ../tarballs +# need to clean up the tarballs dir first because upstream tarball might +# contain a directory with unpredictable name +rm -rf * +git clone --quiet https://github.com/ekg/smithwaterman +cd $ORIGNAME +VERSION=${MVERSION}+`date -d @$(git show --format="%at" | head -n1) +%Y%m%d` +# for esthetical reasons set file timestamps (if git-restore-mtime is installed) +git restore-mtime || true +cd .. +TARDIR=${NAME}-${VERSION} +mv ${ORIGNAME} ${TARDIR} +rm -rf ${TARDIR}/.git + +GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}" +rm -rf ${TARDIR} diff --git a/debian/patches/autoconf.patch b/debian/patches/autoconf.patch new file mode 100644 index 0000000..9113c01 --- /dev/null +++ b/debian/patches/autoconf.patch @@ -0,0 +1,151 @@ +--- /dev/null ++++ b/Makefile.am +@@ -0,0 +1,10 @@ ++lib_LTLIBRARIES = libsmithwaterman.la ++libsmithwaterman_la_SOURCES = BandedSmithWaterman.cpp disorder.cpp IndelAllele.cpp LeftAlign.cpp Repeats.cpp SmithWatermanGotoh.cpp SWMain.cpp ++libsmithwaterman_la_LDFLAGS = -release @VERSION@ ++ ++libsmithwaterman_la_CPPFLAGS = $(INCLUDES) ++ ++bin_PROGRAMS = smithwaterman ++smithwaterman_SOURCES = smithwaterman.cpp ++LDADD = -lsmithwaterman ++ +--- /dev/null ++++ b/configure.ac +@@ -0,0 +1,66 @@ ++# -*- Autoconf -*- ++# Process this file with autoconf to produce a configure script. ++ ++AC_INIT(smithwaterman, 0.0+20151117, [email protected]) ++AC_CONFIG_HEADERS([config.h]) ++ ++AC_PREREQ(2.57) ++ ++# Directory that contains install-sh and other auxiliary files ++AC_CONFIG_AUX_DIR([config]) ++ ++################################################################################ ++# According to (http://www.mail-archive.com/[email protected]/msg14232.html) ++# this macro should be after AC_INIT but before AM_INIT_AUTOMAKE ++################################################################################ ++AC_CONFIG_MACRO_DIR(config) ++ ++AM_INIT_AUTOMAKE([1.6 foreign dist-zip tar-ustar filename-length-max=299]) ++ ++# Checks for programs. ++AC_PROG_LN_S ++AC_PROG_INSTALL ++AC_PROG_LIBTOOL ++ ++################################################################################ ++# calling AC_PROG_CXX resets CXXFLAGS, we use our own flags set in the ++# the AX_CXXFLAGS macro below. ++# So we cache the argument to configure ++# here in ARG_CXX_FLAGS (so that our macro does not override them) ++################################################################################ ++ARG_CXX_FLAGS="$CXXFLAGS" ++AC_PROG_CXX ++ ++#Ranlib handled by check for libtool ++CXXFLAGS="$ARG_CXX_FLAGS" ++AX_CXXFLAGS ++ ++AC_MSG_CHECKING([whether C++ compiler works]) ++AC_LANG_PUSH(C++) ++AC_COMPILE_IFELSE(AC_LANG_PROGRAM([[ ++#include <vector> ++]], [[]]), [compiler_works='yes'], [compiler_works='no']) ++AC_MSG_RESULT([$compiler_works]) ++AC_LANG_POP() ++if test x$compiler_works = xno ++then ++ AC_MSG_ERROR([No functioning C++ compiler found]) ++fi ++ ++ ++AC_SUBST(CXXFLAGS) ++ ++CPPFLAGS="-I\$(top_srcdir) $CPPFLAGS" ++# Checks for libraries. ++ ++# Checks for header files. ++AC_HEADER_STDC ++AC_CHECK_HEADERS([stdlib.h]) ++ ++AC_PROG_MAKE_SET ++ ++AC_CONFIG_FILES([ \ ++ Makefile \ ++ ]) ++AC_OUTPUT ++ +--- a/Makefile ++++ /dev/null +@@ -1,66 +0,0 @@ +-# ========================================= +-# MOSAIK Banded Smith-Waterman Makefile +-# (c) 2009 Michael Stromberg & Wan-Ping Lee +-# ========================================= +- +-# ---------------------------------- +-# define our source and object files +-# ---------------------------------- +-SOURCES= smithwaterman.cpp BandedSmithWaterman.cpp SmithWatermanGotoh.cpp Repeats.cpp LeftAlign.cpp IndelAllele.cpp +-OBJECTS= $(SOURCES:.cpp=.o) disorder.o +-OBJECTS_NO_MAIN= disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o +- +-# ---------------- +-# compiler options +-# ---------------- +- +-# Use ?= to allow overriding from the env or command-line +-CXX?= c++ +-CXXFLAGS?= -O3 +-OBJ?= sw.o +- +-# I don't think := is useful here, since there is nothing to expand +-LDFLAGS:= -Wl,-s +-#CXXFLAGS=-g +-EXE:= smithwaterman +-LIBS= +- +-all: $(EXE) $(OBJ) +- +-.PHONY: all +- +-libsw.a: smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o LeftAlign.o Repeats.o IndelAllele.o disorder.o +- ar rs $@ smithwaterman.o SmithWatermanGotoh.o disorder.o BandedSmithWaterman.o LeftAlign.o Repeats.o IndelAllele.o +- +-sw.o: BandedSmithWaterman.o SmithWatermanGotoh.o LeftAlign.o Repeats.o IndelAllele.o disorder.o +- ld -r $^ -o sw.o -L. +- #$(CXX) $(CFLAGS) -c -o smithwaterman.cpp $(OBJECTS_NO_MAIN) -I. +- +-### @$(CXX) $(LDFLAGS) $(CFLAGS) -o $@ $^ -I. +-$(EXE): smithwaterman.o BandedSmithWaterman.o SmithWatermanGotoh.o disorder.o LeftAlign.o Repeats.o IndelAllele.o +- $(CXX) $(CFLAGS) $^ -I. -o $@ +- +-#smithwaterman: $(OBJECTS) +-# $(CXX) $(CXXFLAGS) -o $@ $< -I. +- +-smithwaterman.o: smithwaterman.cpp disorder.o +- $(CXX) $(CXXFLAGS) -c -o $@ smithwaterman.cpp -I. +- +-disorder.o: disorder.cpp disorder.h +- $(CXX) $(CXXFLAGS) -c -o $@ $< -I. +-BandedSmithWaterman.o: BandedSmithWaterman.cpp BandedSmithWaterman.h +- $(CXX) $(CXXFLAGS) -c -o $@ $< -I. +-SmithWatermanGotoh.o: SmithWatermanGotoh.cpp SmithWatermanGotoh.h disorder.o +- $(CXX) $(CXXFLAGS) -c -o $@ $< -I. +-Repeats.o: Repeats.cpp +- $(CXX) $(CXXFLAGS) -c -o $@ $< -I. +-LeftAlign.o: LeftAlign.cpp +- $(CXX) $(CXXFLAGS) -c -o $@ $< -I. +-IndelAllele.o: IndelAllele.cpp +- $(CXX) $(CXXFLAGS) -c -o $@ $< -I. +- +-.PHONY: clean +- +-clean: +- @echo "Cleaning up." +- @rm -f *.o $(PROGRAM) *~ diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..9ac37bf --- /dev/null +++ b/debian/patches/series @@ -0,0 +1 @@ +autoconf.patch diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..2e15657 --- /dev/null +++ b/debian/rules @@ -0,0 +1,26 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 +export LC_ALL=C.UTF-8 + +# 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. + +# for hardening you might like to uncomment this: +# export DEB_BUILD_MAINT_OPTIONS=hardening=+all + +%: + dh $@ --with autoreconf + +get-orig-source: + . debian/get-orig-source 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..d8b5812 --- /dev/null +++ b/debian/upstream/metadata @@ -0,0 +1,12 @@ +Reference: + Author: + Title: + Journal: + Year: + Volume: + Number: + Pages: + DOI: + PMID: + URL: + eprint: diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..ce144f4 --- /dev/null +++ b/debian/watch @@ -0,0 +1,2 @@ +# version=3 +# Upstream does not tag releases -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libsmithwaterman.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
