[med-svn] [libsmithwaterman] 02/02: Initial packaging until I'm struck with build problems
Andreas Tille
tille at debian.org
Wed Jun 22 11:47:12 UTC 2016
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 <tille at debian.org>
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 <debian-med-packaging at lists.alioth.debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+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 <maintainer at e.mail>
+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 = $(INCLUDES)
++
++bin_PROGRAMS = smithwaterman
++smithwaterman_SOURCES = smithwaterman.cpp
++LDADD = -lsmithwaterman
++
+--- /dev/null
++++ b/configure.ac
+@@ -0,0 +1,66 @@
++# -*- Autoconf -*-
++# Process this file with autoconf to produce a configure script.
++
++AC_INIT(smithwaterman, 0.0+20151117, erik.garrison at bc.edu)
++AC_CONFIG_HEADERS([config.h])
++
++AC_PREREQ(2.57)
++
++# Directory that contains install-sh and other auxiliary files
++AC_CONFIG_AUX_DIR([config])
++
++################################################################################
++# According to (http://www.mail-archive.com/autoconf@gnu.org/msg14232.html)
++# this macro should be after AC_INIT but before AM_INIT_AUTOMAKE
++################################################################################
++AC_CONFIG_MACRO_DIR(config)
++
++AM_INIT_AUTOMAKE([1.6 foreign dist-zip tar-ustar filename-length-max=299])
++
++# Checks for programs.
++AC_PROG_LN_S
++AC_PROG_INSTALL
++AC_PROG_LIBTOOL
++
++################################################################################
++# calling AC_PROG_CXX resets CXXFLAGS, we use our own flags set in the
++# the AX_CXXFLAGS macro below.
++# So we cache the argument to configure
++# here in ARG_CXX_FLAGS (so that our macro does not override them)
++################################################################################
++ARG_CXX_FLAGS="$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
--
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