Michael R. Crusoe pushed to branch master at Debian Med / last-align
Commits: af73543f by Michael R. Crusoe at 2020-05-17T18:15:35+02:00 i386: enable avx2, avx, and sse4.1 specific builds as well - - - - - bcc8c5f6 by Michael R. Crusoe at 2020-05-17T18:15:35+02:00 Demote GNU parallel to a recommends; only used by parallel-fasta - - - - - 3 changed files: - debian/changelog - debian/control - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +last-align (1061-2) UNRELEASED; urgency=medium + + * Team upload. + * i386: enable avx2, avx, and sse4.1 specific builds as well + * Demote GNU parallel to a recommends; only used by parallel-fasta + + -- Michael R. Crusoe <[email protected]> Sun, 17 May 2020 12:32:51 +0200 + last-align (1061-1) unstable; urgency=medium * Team upload. ===================================== debian/control ===================================== @@ -20,9 +20,9 @@ Architecture: any Built-Using: ${Built-Using} Depends: ${shlibs:Depends}, ${misc:Depends}, - parallel Recommends: python3, - python3-pil + python3-pil, + parallel Description: genome-scale comparison of biological sequences LAST is software for comparing and aligning sequences, typically DNA or protein sequences. LAST is similar to BLAST, but it copes better with very ===================================== debian/rules ===================================== @@ -40,7 +40,7 @@ ifeq (amd64,$(DEB_HOST_ARCH)) else ifeq (i386,$(DEB_HOST_ARCH)) mkdir -p $(prefix) mkdir -p $(libexecdir) - for SIMD in ssse3 sse3 sse2 sse mmx; do \ + for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 sse; do \ export CXXFLAGS="$(CXXFLAGS) -m$${SIMD}" && export CFLAGS="$(CFLAGS) -m$${SIMD}" && \ dh_auto_build -- all SFX=-$${SIMD} ; \ find . -name '*.o' -delete ; \ @@ -79,14 +79,14 @@ ifeq (amd64,$(DEB_HOST_ARCH)) for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \ dh_auto_clean -- SFX=-$${SIMD} ; done else ifeq (i386,$(DEB_HOST_ARCH)) - for SIMD in ssse3 sse3 sse2 sse mmx plain; do \ + for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 sse plain; do \ dh_auto_clean -- SFX=-$${SIMD} ; done else dh_auto_clean endif for i in last-merge-batches last-pair-probs last-split last-split8 lastal lastal8 lastdb lastdb8; \ do \ - for j in avx avx2 sse2 sse3 sse4.1 ssse3 ; \ + for j in avx avx2 sse2 sse3 sse4.1 ssse3 sse3 sse2 sse ; \ do \ rm -f src/$$i-$$j ; \ done ; \ @@ -105,7 +105,7 @@ override_dh_installman: --name="genome-scale comparison of biological sequences" \ --help-option="-h" \ $(prefix)/bin/lastal8 > $(mandir)/lastal8.1 - # help2man output needs manual postprocessing - see debian/mans + # help2man output needs manual postprocessing - see debian/mans #$(HELP2MAN) \ # --name="genome-scale comparison of biological sequences" \ # --help-option="-h" \ @@ -116,7 +116,7 @@ override_dh_installman: $(HELP2MAN) \ --name="changes the order of the sequences in MAF-format alignments" \ $(CURDIR)/scripts/maf-swap > $(mandir)/maf-swap.1 - # help2man output needs manual postprocessing - see debian/mans + # help2man output needs manual postprocessing - see debian/mans #$(HELP2MAN) \ # --name="Add extra column with mapping probabilities" \ # $(CURDIR)/scripts/last-map-probs > $(mandir)/last-map-probs.1 @@ -124,7 +124,7 @@ override_dh_installman: #$(HELP2MAN) \ # --name="Read files of lastal output, merge corresponding batches, and write them." \ # $(CURDIR)/scripts/last-merge-batches > $(mandir)/last-merge-batches.1 - # These scripts were droped + # # These scripts were droped #$(HELP2MAN) \ # --name="Clean up MAF-format alignments" \ # $(CURDIR)/scripts/last-reduce-alignments > $(mandir)/last-reduce-alignments.1 @@ -149,7 +149,7 @@ override_dh_installman: $(HELP2MAN) \ --name="Read files of lastal output, merge corresponding batches, and write them" \ $(prefix)/bin/last-merge-batches > $(mandir)/last-merge-batches.1 - # help2man output needs manual postprocessing - see debian/mans + # help2man output needs manual postprocessing - see debian/mans #$(HELP2MAN) \ # --name="Read alignments of paired DNA reads to a genome, and do estimations" \ # $(prefix)/bin/last-pair-probs > $(mandir)/last-pair-probs.1 View it on GitLab: https://salsa.debian.org/med-team/last-align/-/compare/830a97da55db70d0389a90a825c4b2c4d654f5bb...bcc8c5f686990ac3beec20d80595b0168ce0d56c -- View it on GitLab: https://salsa.debian.org/med-team/last-align/-/compare/830a97da55db70d0389a90a825c4b2c4d654f5bb...bcc8c5f686990ac3beec20d80595b0168ce0d56c You're receiving this email because of your account on salsa.debian.org.
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