[med-svn] [Git][med-team/ksw2][master] 6 commits: Use d-shlibs

Andreas Tille gitlab at salsa.debian.org
Fri May 15 11:13:01 BST 2020 


Andreas Tille pushed to branch master at Debian Med / ksw2


Commits:
036df55e by Andreas Tille at 2020-05-15T11:30:49+02:00
Use d-shlibs

- - - - -
6dc9bd8a by Andreas Tille at 2020-05-15T11:44:08+02:00
Try hard to get HAVE_KALLOC defined but failed

- - - - -
acb2700e by Andreas Tille at 2020-05-15T11:45:56+02:00
Fix copyright

- - - - -
c4b01545 by Andreas Tille at 2020-05-15T11:48:17+02:00
Fix yaml

- - - - -
22b89e5e by Andreas Tille at 2020-05-15T12:12:08+02:00
Add conflicts

- - - - -
065e9821 by Andreas Tille at 2020-05-15T12:12:26+02:00
need help how to call this test program with the provided data

- - - - -


9 changed files:

- debian/changelog
- debian/control
- debian/copyright
- − debian/libksw2-0.install
- − debian/libksw2-dev.install
- − debian/libksw2-dev.links
- debian/patches/autoconf.patch
- debian/rules
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -2,4 +2,4 @@ ksw2 (0.0+git20190429.f06f9b3-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #nnnn)
 
- -- Steffen Moeller <moeller at debian.org>  Thu, 14 May 2020 20:48:41 +0200
+ -- Andreas Tille <tille at debian.org>  Fri, 15 May 2020 11:45:35 +0200


=====================================
debian/control
=====================================
@@ -1,24 +1,29 @@
 Source: ksw2
-Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller at debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>,
+           Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
 Build-Depends: debhelper-compat (= 12),
+               d-shlibs,
                autoconf-archive,
                pkg-config,
                zlib1g-dev
 Standards-Version: 4.5.0
-Section: libs
-Homepage: https://github.com/lh3/ksw2
 Vcs-Browser: https://salsa.debian.org/med-team/ksw2
 Vcs-Git: https://salsa.debian.org/med-team/ksw2.git
+Homepage: https://github.com/lh3/ksw2
 Rules-Requires-Root: no
 
 Package: libksw2-dev
-Section: libdevel
 Architecture: any
 Multi-Arch: same
-Depends: libksw20 (= ${binary:Version}), ${misc:Depends}
-Description: globl alignment and alignment extension library
+Section: libdevel
+Depends: libksw2-0 (= ${binary:Version}),
+         ${misc:Depends}
+Conflicts: libminimap2-dev (<= 2.17+dfsg-9)
+Replaces: libminimap2-dev (<= 2.17+dfsg-9)
+Description: globl alignment and alignment extension library (development)
  KSW2 is a library to align a pair of biological sequences based on
  dynamic programming (DP). So far it comes with global alignment and
  alignment extension (no local alignment yet) under an affine gap cost
@@ -39,10 +44,35 @@ Description: globl alignment and alignment extension library
  KSW2 implements the Suzuki-Kasahara algorithm and is a component of minimap2.
  The exact situation is a bit unclear though since these files are shipping
  with more recent modifications in the minimap2 source tree.
+ .
+ This package contains the static library and header files.
 
 Package: libksw2-0
 Architecture: any
 Multi-Arch: same
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: globl alignment and alignment extension - header files
- Header files for the KSW2 library for the comparison of biological sequences.
+Section: libs
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: globl alignment and alignment extension
+ KSW2 is a library to align a pair of biological sequences based on
+ dynamic programming (DP). So far it comes with global alignment and
+ alignment extension (no local alignment yet) under an affine gap cost
+ function: gapCost(k) = q+k*e, or a two-piece affine gap cost: gapCost2(k)
+ = min{q+k*e, q2+k*e2}. For the latter cost function, if q+e<q2+e2 and
+ e>e2, (q,e) is effectively applied to short gaps only, while (q2,e2)
+ applied to gaps no shorter than ceil((q2-q)/(e-e2)-1). It helps to
+ retain long gaps. The algorithm behind the two-piece cost is close to
+ Gotoh (1990).
+ .
+ KSW2 supports fixed banding and optionally produces alignment paths
+ (i.e. CIGARs) with gaps either left- or right-aligned. It provides
+ implementations using SSE2 and SSE4.1 intrinsics based on Hajime
+ Suzuki's diagonal formulation which enables 16-way SSE parallelization
+ for the most part of the inner loop, regardless of the maximum score
+ of the alignment.
+ .
+ KSW2 implements the Suzuki-Kasahara algorithm and is a component of minimap2.
+ The exact situation is a bit unclear though since these files are shipping
+ with more recent modifications in the minimap2 source tree.
+ .
+ This package contains the dynamic library.


=====================================
debian/copyright
=====================================
@@ -8,7 +8,6 @@ Copyright: 2017-2019 Heng Li <lh3 at me.com>
 License: MIT
 
 Files: kseq.h
-       kseq.c
 Copyright: 2008, 2009, 2011 Attractive Chaos <attractor at live.co.uk>
 License: MIT
 


=====================================
debian/libksw2-0.install deleted
=====================================
@@ -1 +0,0 @@
-lib*so*	usr/lib


=====================================
debian/libksw2-dev.install deleted
=====================================
@@ -1 +0,0 @@
-*.h	usr/include/ksw2/


=====================================
debian/libksw2-dev.links deleted
=====================================
@@ -1 +0,0 @@
-usr/lib/libksw2.so.0	usr/lib/libksw2.so


=====================================
debian/patches/autoconf.patch
=====================================
@@ -22,7 +22,7 @@
 +
 --- /dev/null
 +++ b/configure.ac
-@@ -0,0 +1,68 @@
+@@ -0,0 +1,69 @@
 +#                                               -*- Autoconf -*-
 +# Process this file with autoconf to produce a configure script.
 +
@@ -82,7 +82,8 @@
 +
 +AC_PROG_MAKE_SET
 +
-+AC_DEFINE([HAVE_KALLOC], [], [Use ksw2's own malloc functions])
++dnl AC_DEFINE([HAVE_KALLOC], [1], [Use ksw2 own malloc functions])
++AC_CHECK_HEADER([kalloc.h], [AC_DEFINE([HAVE_KALLOC], [1], [Use ksw2 own malloc functions])] )
 +
 +AC_CONFIG_FILES([
 +	Makefile


=====================================
debian/rules
=====================================
@@ -1,8 +1,6 @@
 #!/usr/bin/make -f
 export DH_VERBOSE = 1
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-#export DEB_CFLAGS_MAINT_APPEND  = -Wall -pedantic
-#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
 
 %:
 	dh $@
@@ -15,3 +13,20 @@ override_dh_autoreconf:
 override_dh_auto_install:
 	dh_auto_install
 	rm ax_check_zlib.m4
+# FIXME: End of dirty hack.
+
+override_dh_install:
+	dh_install
+	d-shlibmove --commit \
+		    --multiarch \
+		    --devunversioned \
+		    --exclude-la \
+		    --movedev debian/tmp/usr/include usr \
+		    --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig \
+		    debian/tmp/usr/lib/*/*.so
+
+# FIXME: need help how to call this test program with the provided data
+#override_dh_auto_test:
+#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+#	ksw2-test
+#endif


=====================================
debian/upstream/metadata
=====================================
@@ -1,18 +1,21 @@
 Reference:
  - Author: H. Suzuki and M. Kasahara
-   Title: Introducing difference recurrence relations for faster semi-global alignment of long sequences
+   Title: >
+     Introducing difference recurrence relations for faster semi-global
+     alignment of long sequences
    Journal: BMC Bioinformatics
    Year: 2018
    Volume: 19
    Pages: 45
-   DOI: 10.1186/s12859-018-2014-8 
+   DOI: 10.1186/s12859-018-2014-8
    PMID: 29504909
    PMCID: PMC5836832
    URL: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2014-8
    eprint: https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2014-8
- - Author: Li, H.
-   Year: 2018
-   Title: Minimap2: pairwise alignment for nucleotide sequences.
+ - Author: H. Li
+   Title: >
+     Minimap2: pairwise alignment for nucleotide sequences
    Journal: Bioinformatics
+   Year: 2018
    Volume: 34
    Pages: 3094-3100



View it on GitLab: https://salsa.debian.org/med-team/ksw2/-/compare/283fc286a1f27a345cecd9f31e5201e12f6716b4...065e9821653b88bd0b5b54a3d184dfd86fb84f2a

-- 
View it on GitLab: https://salsa.debian.org/med-team/ksw2/-/compare/283fc286a1f27a345cecd9f31e5201e12f6716b4...065e9821653b88bd0b5b54a3d184dfd86fb84f2a
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200515/c1e02036/attachment-0001.html>

More information about the debian-med-commit mailing list