debian/control

@@ -4,13 +4,17 @@ Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 12~),
+               d-shlibs,
+               pkg-config,
+               zlib1g-dev
 Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/libmaus2
 Vcs-Git: https://salsa.debian.org/med-team/libmaus2.git
 Homepage: https://gitlab.com/german.tischler/libmaus2
 
-Package: libmaus2
+Package: libmaus2-2
 Architecture: any
+Section: libs
 Depends: ${shlibs:Depends},
          ${misc:Depends}
 Description: collection of data structures and algorithms for biobambam
@@ -22,3 +26,19 @@ Description: collection of data structures and algorithms for biobambam
   * BAM sequence alignment files input/output (simple and collating)
  .
  and many lower level support classes.
+
+Package: libmaus2-dev
+Architecture: any
+Section: libdevel
+Depends: libmaus2-2 (= ${binary:Version}),
+         ${shlibs:Depends},
+         ${misc:Depends}
+Description: collection of data structures and algorithms for biobambam
+ Libmaus2 is a collection of data structures and algorithms. It contains
+ .
+  * I/O classes (single byte and UTF-8)
+  * bitio classes (input, output and various forms of bit level manipulation)
+  * text indexing classes (suffix and LCP array, fulltext and minute (FM), ...)
+  * BAM sequence alignment files input/output (simple and collating)
+ .
+ and many lower level support classes.

debian/copyright

@@ -3,9 +3,49 @@ Upstream-Name: libmaus2
 Source: https://gitlab.com/german.tischler/libmaus2/tags
 
 Files: *
-Copyright: 20xx-20yy <upstream>
-License: <license>
+Copyright: 2010-2016 German Tischler
+License: GPL-3+
+
+Files: src/libmaus2/hashing/hash.hpp
+Copyright: 1996, Bob Jenkins <bob_jenkins@burtleburtle.net>
+License: public_domain
+ You may use this code any way you wish, private, educational, or commercial.
+ It's free.
+
+Files: src/libmaus2/lcp/OracleLCP*
+Copyright: 2008 Simon Puglisi
+           2009-2013 German Tischler
+           2011-2013 Genome Research Limited
+License: GPL-3+
+
+Files: src/libmaus2/rmq/FischerSystematicSuccinctRMQ*
+Copyright: 2010 Johannes Fischer
+           2010-2013 German Tischler
+           2011-2013 Genome Research Limited
+License: GPL-3+
+
+Files: src/libmaus2/util/NearestNeighbourDictionary.*
+       src/libmaus2/bp/BalancedParenthesesBase.hpp
+Copyright: 2007-2012 Simon Gog (SDSL library)
+           2009-2013 German Tischler
+           2011-2013 Genome Research Limited
+License: GPL-3
+
+radixsort code in src/libmaus2/sorting/SerialRadixSort64.hpp adapted from code by Andrew I. Schein (see file for license)
+divsufsort code in src/libmaus2/suffixsort/divsufsort* by Yuta Mori (see file for license)
+SAIS code in src/libmaus2/suffixsort/SAIS_Mori.hpp by Yuta Mori (see file for license)
+md5 code in src/libmaus2/digest/md5.[ch] by L. Peter Deutsch (Aladdin Enterprises) (see file for license)
+some code in src/libmaus2/bambam/DuplicationMetrics.hpp is imported from the Picard project (MIT license, see file for copyright)
+LZ4 code in src/libmaus2/lz/lz4.[ch] by Yann Collect (BSD 2-Clause licence, see files)
+CRC32 code in src/libmaus2/hashing/Crc3.{cpp/hpp} by Stephan Brumme (ZLib type license, see files)
+libmaus2/digest/sha(256|512)_*.asm (Intel license, see files)
+Part of CRC32{|C} code in src/libmaus2/digest/CRC32{|C}_Core.cpp by Mark Adler (see file for license)
+Part of CRC32{|C} code in src/libmaus2/digest/CRC32{|C}_Core.cpp by Cisco Systems, Inc. and Herbert Xu (GPLv2)
+Hash code in src/libmaus2/hashing/MurmurHash3.{cpp|h} and libmaus2/digest/MurmurHash3_x64_128.hpp by Austin Appleby (public domain)
+Rest by German Tischler published under GPLv2/GPLv3 (some of it written while at Genome Research Limited/WTSI)
+
+
 
 Files: debian/*
 Copyright: 2019 Andreas Tille <tille@debian.org>
-License: <license>
+License: GPL-3+

debian/libmaus2-2.install

+usr/lib/*/libmaus2*.so.*
+usr/lib/*/libmaus2/2.*/libmaus2_scram_mod.so

debian/libmaus2-dev.install

+usr/lib/*/libmaus2*.a
+usr/lib/*/libmaus2*.so

debian/lintian-overrides

-# see https://lists.debian.org/debian-med/2018/06/msg00043.html
-#PKGNAME#: script-with-language-extension usr/bin/*.*

debian/rules

@@ -3,16 +3,7 @@
 # DH_VERBOSE := 1
 export LC_ALL=C.UTF-8
 
-include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
-# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
-#                    specified by <https://reproducible-builds.org/specs/source-date-epoch/>
+# include /usr/share/dpkg/default.mk
 
 # for hardening you might like to uncomment this:
 # export DEB_BUILD_MAINT_OPTIONS=hardening=+all
@@ -20,12 +11,27 @@ include /usr/share/dpkg/default.mk
 %:
 	dh $@
 
+override_dh_install:
+	dh_install
+	d-shlibmove --commit \
+		    --multiarch \
+		    --devunversioned \
+		    --exclude-la \
+		    --movedev debian/tmp/usr/include/* usr/include \
+		    --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig \
+		    debian/tmp/usr/lib/*/*.so
+	# Remove unneeded options from *.pc files
+	find debian -name "*.pc" -exec sed -i -e 's/-Wdate-time *//' -e 's/-D_FORTIFY_SOURCE=2 *//' \{\} \;
+	# avoid noise from dh-missing by deleting unneeded files
+	find debian/tmp -type f -name "*.la" -delete
+	# Changelog is installed via dh_installchangelogs
+	rm -f debian/tmp/usr/share/doc/libmaus2/changelog.gz
+
+override_dh_installchangelogs:
+	dh_installchangelogs ChangeLog
+
 ### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
 #override_dh_auto_test:
 #ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 #	do_stuff_for_testing
 #endif
-
-### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script
-#get-orig-source:
-#	. debian/get-orig-source