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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
