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 <[email protected]> Thu, 14 May 2020 20:48:41 +0200 + -- Andreas Tille <[email protected]> Fri, 15 May 2020 11:45:35 +0200 ===================================== debian/control ===================================== @@ -1,24 +1,29 @@ Source: ksw2 -Priority: optional Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Steffen Moeller <[email protected]> +Uploaders: Steffen Moeller <[email protected]>, + Andreas Tille <[email protected]> +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 <[email protected]> License: MIT Files: kseq.h - kseq.c Copyright: 2008, 2009, 2011 Attractive Chaos <[email protected]> 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.
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