[med-svn] [libtabixpp] 03/03: flesh out package a bit
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Sun Dec 6 18:59:41 UTC 2015
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository libtabixpp.
commit 457e505cc279d76a16b62fc7557a5ad3059f2133
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Sun Dec 6 18:59:23 2015 +0000
flesh out package a bit
---
debian/README.license | 3 ++
debian/changelog | 4 +-
debian/control | 32 +++++++++++----
debian/libtabixpp-dev.links | 1 +
debian/patches/build_with_debian_htslib.patch | 58 +++++++++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 22 +++-------
7 files changed, 95 insertions(+), 26 deletions(-)
diff --git a/debian/README.license b/debian/README.license
new file mode 100644
index 0000000..dde526c
--- /dev/null
+++ b/debian/README.license
@@ -0,0 +1,3 @@
+This package does not yet have a license defined by upstream.
+
+ss34, 20151206
diff --git a/debian/changelog b/debian/changelog
index 5125bdd..37d71b5 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
-libtabixpp (0.0.20141119-1) UNRELEASED; urgency=low
+libtabixpp (0.0.20151117-1) UNRELEASED; urgency=low
* Initial release (Closes: #<bug>)
- -- Andreas Tille <tille at debian.org> Sun, 01 Feb 2015 14:56:48 +0100
+ -- Sascha Steinbiss <sascha at steinbiss.name> Sun, 06 Dec 2015 18:22:18 +0000
diff --git a/debian/control b/debian/control
index 309e806..4a7d1b7 100644
--- a/debian/control
+++ b/debian/control
@@ -2,24 +2,40 @@ Source: libtabixpp
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Sascha Steinbiss <sascha at steinbiss.name>
Build-Depends: debhelper (>= 9),
- python-markdown,
+ libhts-dev,
+ libhts1,
+ zlib1g,
zlib1g-dev
Standards-Version: 3.9.6
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libtabixpp.git
Vcs-Git: git://anonscm.debian.org/debian-med/libtabixpp.git
Homepage: https://github.com/ekg/tabixpp
-Package: libtabixpp
+Package: libtabixpp0
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Section: libs
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
Description: C++ wrapper to tabix indexer
Tabix indexes files where some columns indicate sequence coordinates: name
- (usually a chromosme), start and stop. The input data file must be position
+ (usually a chromosome), start and stop. The input data file must be position
sorted and compressed by bgzip (provided in this package), which has a gzip
- like interface. After indexing, tabix is able to quickly retrieve data lines by
- chromosomal coordinates. Fast data retrieval also works over network if an URI
- is given as a file name.
+ like interface. After indexing, tabix is able to quickly retrieve data lines
+ by chromosomal coordinates. Fast data retrieval also works over network if an
+ URI is given as a file name.
.
This package provides a C++ wrapper to the tabix indexer.
+
+Package: libtabixpp-dev
+Architecture: any
+Section: libdevel
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ libtabixpp0 (= ${binary:Version})
+Description: C++ wrapper to tabix indexer (development files)
+ This package provides development headers and static libraries for libtabixpp,
+ a C++ interface wrapper for Tabix. Tabix is a part of htslib to index tabular
+ files in which some columns indicate sequence coordinates.
\ No newline at end of file
diff --git a/debian/libtabixpp-dev.links b/debian/libtabixpp-dev.links
new file mode 100644
index 0000000..35903fa
--- /dev/null
+++ b/debian/libtabixpp-dev.links
@@ -0,0 +1 @@
+usr/lib/libtabixpp.so.0 usr/lib/libtabixpp.so
\ No newline at end of file
diff --git a/debian/patches/build_with_debian_htslib.patch b/debian/patches/build_with_debian_htslib.patch
new file mode 100644
index 0000000..9bcba7e
--- /dev/null
+++ b/debian/patches/build_with_debian_htslib.patch
@@ -0,0 +1,58 @@
+Description: Build_with_debian_htslib
+--- a/Makefile
++++ b/Makefile
+@@ -3,11 +3,12 @@
+
+ CC?= gcc
+ CXX?= g++
+-CXXFLAGS?= -g -Wall -O2 -fPIC #-m64 #-arch ppc
++CXXFLAGS+= -fPIC
+ INCLUDES?= -Ihtslib
+ HTS_HEADERS?= htslib/htslib/bgzf.h htslib/htslib/tbx.h
+ HTS_LIB?= htslib/libhts.a
+ LIBPATH?= -L. -Lhtslib
++SONUMBER=0
+
+ DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
+ PROG= tabix++
+@@ -18,32 +19,21 @@
+ .c.o:
+ $(CC) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+
+-all-recur lib-recur clean-recur cleanlocal-recur install-recur:
+- @target=`echo $@ | sed s/-recur//`; \
+- wdir=`pwd`; \
+- list='$(SUBDIRS)'; for subdir in $$list; do \
+- cd $$subdir; \
+- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CXXFLAGS="$(CXXFLAGS)" \
+- INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target \
+- || exit 1; \
+- cd $$wdir; \
+- done;
++all: $(PROG) libtabixpp.so.$(SONUMBER)
+
+-all: $(PROG)
+-
+-tabix.o: $(HTS_HEADERS) tabix.cpp tabix.hpp
++tabix.o: tabix.cpp tabix.hpp
+ $(CXX) $(CXXFLAGS) -c tabix.cpp $(INCLUDES)
+
+-htslib/libhts.a:
+- cd htslib && $(MAKE) lib-static
++libtabixpp.so.$(SONUMBER): tabix.o
++ $(CC) $(LDFLAGS) $(CXXFLAGS) -Wl,-soname,libtabixpp.so.$(SONUMBER) -shared -o $@ $<
+
+-tabix++: tabix.o main.cpp $(HTS_LIB)
++tabix++: tabix.o main.cpp
+ $(CXX) $(CXXFLAGS) -o $@ main.cpp tabix.o $(INCLUDES) $(LIBPATH) \
+ -lhts -lpthread -lm -lz
+
+ cleanlocal:
+ rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a tabix.aux tabix.log \
+- tabix.pdf *.class libtabix.*.dylib libtabix.so*
+- cd htslib && $(MAKE) clean
++ tabix.pdf *.class libtabix*.dylib libtabix*so*
++ #cd htslib && $(MAKE) clean
+
+-clean:cleanlocal-recur
++clean: cleanlocal
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..d9842e9
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+build_with_debian_htslib.patch
diff --git a/debian/rules b/debian/rules
index 58ec00b..54b17b5 100755
--- a/debian/rules
+++ b/debian/rules
@@ -2,22 +2,12 @@
# 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/cdbs/1/rules/buildvars.mk
-# and use what is set there. Any hint whether dh might set variables in
-# a similar manner are welcome.
-
%:
dh $@
-#get-orig-source:
-# . debian/get-orig-source
+override_dh_auto_install:
+ mkdir -p debian/libtabixpp-dev/usr/include
+ cp *hpp debian/libtabixpp-dev/usr/include
+ mkdir -p debian/libtabixpp0/usr/lib
+ cp libtabixpp.so* debian/libtabixpp0/usr/lib/
+ dh_auto_install --
\ No newline at end of file
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libtabixpp.git
More information about the debian-med-commit
mailing list