[med-svn] [Git][med-team/minimap2][master] Introducing -dev package

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / minimap2


Commits:
53883a7f by Steffen Moeller at 2020-03-14T23:08:15+01:00
Introducing -dev package

- - - - -


8 changed files:

- debian/changelog
- debian/control
- + debian/libminimap2-dev.dirs
- + debian/libminimap2-dev.install
- debian/install → debian/minimap2.install
- + debian/patches/addLTO.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+minimap2 (2.17+dfsg-3) unstable; urgency=medium
+
+  [Steffen Moeller]
+  * Team upload
+  * Created -dev package
+  * Standards-Version: 4.5.0
+  * Added Link-Time-Optimization
+
+ -- Steffen Moeller <moeller at debian.org>  Sat, 14 Mar 2020 22:45:44 +0100
+
 minimap2 (2.17+dfsg-2) unstable; urgency=medium
 
   [ Michael R. Crusoe ]


=====================================
debian/control
=====================================
@@ -11,7 +11,7 @@ Build-Depends: debhelper-compat (= 12),
                texlive-font-utils,
                ghostscript,
                gnuplot
-Standards-Version: 4.4.1
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/minimap2
 Vcs-Git: https://salsa.debian.org/med-team/minimap2.git
 Homepage: https://github.com/lh3/minimap2
@@ -39,3 +39,23 @@ Description: versatile pairwise aligner for genomic and spliced nucleotide seque
  short reads, minimap2 is three times as fast as BWA-MEM and Bowtie2, and
  as accurate on simulated data. Detailed evaluations are available from
  the minimap2 paper or the preprint.
+
+Package: libminimap2-dev
+Architecture: any
+Section: libdevel
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         zlib1g-dev
+Description: development headers for libminimap
+ Minimap2 is a versatile sequence alignment program that aligns DNA or
+ mRNA sequences against a large reference database. Typical use cases
+ include: (1) mapping PacBio or Oxford Nanopore genomic reads to the
+ human genome; (2) finding overlaps between long reads with error rate up
+ to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA
+ or Direct RNA reads against a reference genome; (4) aligning Illumina
+ single- or paired-end reads; (5) assembly-to-assembly alignment; (6) full-
+ genome alignment between two closely related species with divergence
+ below ~15%.
+ .
+ This package contains the C library headers for using minimap in custom tools,
+ along with a static library.


=====================================
debian/libminimap2-dev.dirs
=====================================
@@ -0,0 +1 @@
+usr/lib


=====================================
debian/libminimap2-dev.install
=====================================
@@ -0,0 +1 @@
+*.a	usr/lib/


=====================================
debian/install → debian/minimap2.install
=====================================


=====================================
debian/patches/addLTO.patch
=====================================
@@ -0,0 +1,26 @@
+Index: minimap2/Makefile
+===================================================================
+--- minimap2.orig/Makefile
++++ minimap2/Makefile
+@@ -1,10 +1,11 @@
+-CFLAGS+=		-g -Wall -O2 -Wc++-compat #-Wextra
++CFLAGS+=	-g -Wall -O2 -Wc++-compat -flto #-Wextra
+ CPPFLAGS+=	-DHAVE_KALLOC
+ INCLUDES=
+ OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o
+ PROG=		minimap2
+ PROG_EXTRA=	sdust minimap2-lite
+ LIBS=		-lm -lz -lpthread
++LDFLAGS+=	-flto
+ 
+ OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o
+ 
+@@ -29,7 +30,7 @@ all:$(PROG)
+ extra:all $(PROG_EXTRA)
+ 
+ minimap2:main.o libminimap2.a
+-		$(CC) $(CFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS) $(LDFLAGS)
++		$(CC) main.o -o $@ -L. -lminimap2 $(LIBS) $(LDFLAGS)
+ 
+ minimap2-lite:example.o libminimap2.a
+ 		$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS) $(LDFLAGS)


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 hardening.patch
 do_not_use_natbib.bst.patch
 simde
+addLTO.patch


=====================================
debian/rules
=====================================
@@ -1,6 +1,8 @@
 #!/usr/bin/make -f
 
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+# from minimap 1
+#export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
 include /usr/share/dpkg/architecture.mk
 export DEB_CFLAGS_MAINT_APPEND += -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
 
@@ -31,3 +33,9 @@ endif
 
 override_dh_compress:
 	dh_compress --exclude=.pdf
+
+override_dh_auto_clean:
+	dh_auto_clean
+	rm -f MT-human.mmi
+	rm -f tex/minimap2.aux tex/minimap2.bbl tex/minimap2.blg tex/minimap2.log tex/minimap2.out tex/minimap2.pdf
+



View it on GitLab: https://salsa.debian.org/med-team/minimap2/-/commit/53883a7ff8c066c14c0ea4e42299ae9958feda6a

-- 
View it on GitLab: https://salsa.debian.org/med-team/minimap2/-/commit/53883a7ff8c066c14c0ea4e42299ae9958feda6a
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