[med-svn] [Git][med-team/mmseqs2][master] 5 commits: Build-depend on libsimde-dev 0.6.0-2 to get i386 patches from upstream
Michael R. Crusoe
gitlab at salsa.debian.org
Wed Sep 2 12:17:58 BST 2020
Michael R. Crusoe pushed to branch master at Debian Med / mmseqs2
Commits:
df23200b by Michael R. Crusoe at 2020-09-02T12:23:25+02:00
Build-depend on libsimde-dev 0.6.0-2 to get i386 patches from upstream
- - - - -
b09322a0 by Michael R. Crusoe at 2020-09-02T12:51:42+02:00
fix for i386
- - - - -
21e5e1fc by Michael R. Crusoe at 2020-09-02T13:16:52+02:00
debian/patches/spelling: fix typos
- - - - -
15219931 by Michael R. Crusoe at 2020-09-02T13:16:53+02:00
typo
- - - - -
6f59a6b8 by Michael R. Crusoe at 2020-09-02T13:17:25+02:00
release 12-113e3+ds-1
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/simde_tweak
- + debian/patches/spelling
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,12 +1,13 @@
-mmseqs2 (12-113e3+ds-1) UNRELEASED; urgency=medium
+mmseqs2 (12-113e3+ds-1) unstable; urgency=medium
* Team upload.
* New upstream version
* Freshen debian/copyright
* debian/rules: Ensure all for-loops fail if there is an error
- * i386 build currently broken due to https://github.com/simd-everywhere/simde/issues/607
+ * Build-depend on libsimde-dev 0.6.0-2 to get i386 patches from upstream
+ * debian/patches/spelling: fix typos
- -- Michael R. Crusoe <crusoe at debian.org> Tue, 01 Sep 2020 14:39:02 +0200
+ -- Michael R. Crusoe <crusoe at debian.org> Wed, 02 Sep 2020 13:17:12 +0200
mmseqs2 (11-e1a1c+ds-4) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -9,7 +9,7 @@ Build-Depends-Arch: cmake,
libzstd-dev,
zlib1g-dev,
libbz2-dev,
- libsimde-dev
+ libsimde-dev (>= 0.6.0-2)
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/mmseqs2
Vcs-Git: https://salsa.debian.org/med-team/mmseqs2.git
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,5 @@
+spelling
+simde_tweak
fix_tests.patch
fix_util_installation.patch
use_system_zstd.patch
=====================================
debian/patches/simde_tweak
=====================================
@@ -0,0 +1,64 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
+Subject: work around SIMDe NATIVE_ALIASES issue
+Forwarded: not-needed
+--- mmseqs2.orig/src/commons/Util.cpp
++++ mmseqs2/src/commons/Util.cpp
+@@ -597,41 +597,42 @@
+
+ // Compute reverse complement of k-mer in 2-bit-per-nucleotide encoding (A: 00, C: 01, T: 10, G: 11)
+ uint64_t Util::revComplement(const uint64_t kmer, const int k) {
++
+ // broadcast 64bit to 128 bit
+- __m128i x = _mm_cvtsi64_si128(kmer);
+- __m128i x_up = _mm_cvtsi64_si128(kmer >> (uint64_t)4); // shift right by 2 nucleotides
++ simde__m128i x = simde_mm_cvtsi64_si128(kmer);
++ simde__m128i x_up = simde_mm_cvtsi64_si128(kmer >> (uint64_t)4); // shift right by 2 nucleotides
+
+ // create lookup (set 16 bytes in 128 bit)
+ // a lookup entry at the index of two nucleotides (4 bit) describes the reverse
+ // complement of these two nucleotide in the higher 4 bits (lookup1) or in the lower 4 bits (lookup2)
+ #define c (signed char)
+- __m128i lookup1 = _mm_set_epi8(c(0x50),c(0x10),c(0xD0),c(0x90),c(0x40),c(0x00),c(0xC0),c(0x80),
++ simde__m128i lookup1 = simde_mm_set_epi8(c(0x50),c(0x10),c(0xD0),c(0x90),c(0x40),c(0x00),c(0xC0),c(0x80),
+ c(0x70),c(0x30),c(0xF0),c(0xB0),c(0x60),c(0x20),c(0xE0),c(0xA0));
+- __m128i lookup2 = _mm_set_epi8(c(0x05),c(0x01),c(0x0D),c(0x09),c(0x04),c(0x00),c(0x0C),c(0x08),
++ simde__m128i lookup2 = simde_mm_set_epi8(c(0x05),c(0x01),c(0x0D),c(0x09),c(0x04),c(0x00),c(0x0C),c(0x08),
+ c(0x07),c(0x03),c(0x0F),c(0x0B),c(0x06),c(0x02),c(0x0E),c(0x0A));
+ // set upper 8 bytes to 0 and revert order of lower 8 bytes
+- __m128i upper = _mm_set_epi8(c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),
++ simde__m128i upper = simde_mm_set_epi8(c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),
+ 0,1,2,3,4,5,6,7);
+- // _mm_set1_epi8: create 128 bit with all bytes set to given value
++ // simde_mm_set1_epi8: create 128 bit with all bytes set to given value
+ // here: 0x0F (00001111) and 0xF0 (11110000)
+- // _mm_and_si128: bitwise AND
+- __m128i kmer1 = _mm_and_si128(x, _mm_set1_epi8(c(0x0F))); // get lower 4 bits
+- __m128i kmer2 = _mm_and_si128(x_up, _mm_set1_epi8(c(0x0F))); // get higher 4 bits
++ // simde_mm_and_si128: bitwise AND
++ simde__m128i kmer1 = simde_mm_and_si128(x, simde_mm_set1_epi8(c(0x0F))); // get lower 4 bits
++ simde__m128i kmer2 = simde_mm_and_si128(x_up, simde_mm_set1_epi8(c(0x0F))); // get higher 4 bits
+ #undef c
+
+- // use _mm_shuffle_epi8 to look up reverse complement
+- kmer1 = _mm_shuffle_epi8(lookup1, kmer1);
+- kmer2 = _mm_shuffle_epi8(lookup2, kmer2);
++ // use simde_mm_shuffle_epi8 to look up reverse complement
++ kmer1 = simde_mm_shuffle_epi8(lookup1, kmer1);
++ kmer2 = simde_mm_shuffle_epi8(lookup2, kmer2);
+
+- // _mm_or_si128: bitwise OR
+- x = _mm_or_si128(kmer1, kmer2);
++ // simde_mm_or_si128: bitwise OR
++ x = simde_mm_or_si128(kmer1, kmer2);
+
+ // set upper 8 bytes to 0 and revert order of lower 8 bytes
+- x = _mm_shuffle_epi8(x, upper);
++ x = simde_mm_shuffle_epi8(x, upper);
+
+ // shift out the unused nucleotide positions (1 <= k <=32 )
+ // broadcast 128 bit to 64 bit
+- return (((uint64_t)_mm_cvtsi128_si64(x)) >> (uint64_t)(64-2*k));
++ return (((uint64_t)simde_mm_cvtsi128_si64(x)) >> (uint64_t)(64-2*k));
+
+ }
+
=====================================
debian/patches/spelling
=====================================
@@ -0,0 +1,113 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Spelling typos fixes
+--- mmseqs2.orig/data/workflow/searchslicedtargetprofile.sh
++++ mmseqs2/data/workflow/searchslicedtargetprofile.sh
+@@ -69,7 +69,7 @@
+ fi
+
+ # predict NUM_SEQS_THAT_SATURATE as the average number of prefilter results per profile in previous steps
+- # this allows to increase NUM_PROFS_IN_STEP
++ # this allows one to increase NUM_PROFS_IN_STEP
+ if [ "${NUM_PREF_RESULTS_IN_ALL_PREV_STEPS}" -gt 0 ]; then
+ # BE MORE CAUTIOUS?
+ NUM_PROFS_PROCESSED="$((FIRST_INDEX_LINE-1))"
+--- mmseqs2.orig/src/MMseqsBase.cpp
++++ mmseqs2/src/MMseqsBase.cpp
+@@ -717,7 +717,7 @@
+ {"DB", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::allDb },
+ {"DB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA | DbType::VARIADIC, &DbValidator::allDb }}},
+ {"subtractdbs", subtractdbs, &par.subtractdbs, COMMAND_SET,
+- "Remove all entries from first DB occuring in second DB by key",
++ "Remove all entries from first DB occurring in second DB by key",
+ NULL,
+ "Martin Steinegger <martin.steinegger at snu.ac.kr>",
+ "<i:resultDBLeft> <i:resultDBRight> <o:resultDB>",
+--- mmseqs2.orig/src/commons/DBReader.cpp
++++ mmseqs2/src/commons/DBReader.cpp
+@@ -1106,7 +1106,7 @@
+ if (idx != std::string::npos) {
+ ext = names[i].substr(idx);
+ } else {
+- Debug(Debug::ERROR) << "File extention was not found but it is expected to be there!\n"
++ Debug(Debug::ERROR) << "File extension was not found but it is expected to be there!\n"
+ << "Filename: " << names[i] << ".\n";
+ EXIT(EXIT_FAILURE);
+ }
+--- mmseqs2.orig/src/commons/Parameters.cpp
++++ mmseqs2/src/commons/Parameters.cpp
+@@ -87,7 +87,7 @@
+ PARAM_FORMAT_OUTPUT(PARAM_FORMAT_OUTPUT_ID, "--format-output", "Format alignment output", "Choose comma separated list of output columns from: query,target,evalue,gapopen,pident,fident,nident,qstart,qend,qlen\ntstart,tend,tlen,alnlen,raw,bits,cigar,qseq,tseq,qheader,theader,qaln,taln,qframe,tframe,mismatch,qcov,tcov\nqset,qsetid,tset,tsetid,taxid,taxname,taxlineage,qorfstart,qorfend,torfstart,torfend", typeid(std::string), (void *) &outfmt, ""),
+ PARAM_DB_OUTPUT(PARAM_DB_OUTPUT_ID, "--db-output", "Database output", "Return a result DB instead of a text file", typeid(bool), (void *) &dbOut, "", MMseqsParameter::COMMAND_EXPERT),
+ // --include-only-extendablediagonal
+- PARAM_RESCORE_MODE(PARAM_RESCORE_MODE_ID, "--rescore-mode", "Rescore mode", "Rescore diagonals with:\n0: Hamming distance\n1: local alignment (score only)\n2: local alignment\n3: global alignment\n4: longest alignment fullfilling window quality criterion", typeid(int), (void *) &rescoreMode, "^[0-4]{1}$"),
++ PARAM_RESCORE_MODE(PARAM_RESCORE_MODE_ID, "--rescore-mode", "Rescore mode", "Rescore diagonals with:\n0: Hamming distance\n1: local alignment (score only)\n2: local alignment\n3: global alignment\n4: longest alignment fulfilling window quality criterion", typeid(int), (void *) &rescoreMode, "^[0-4]{1}$"),
+ PARAM_WRAPPED_SCORING(PARAM_WRAPPED_SCORING_ID, "--wrapped-scoring", "Allow wrapped scoring", "Double the (nucleotide) query sequence during the scoring process to allow wrapped diagonal scoring around end and start", typeid(bool), (void *) &wrappedScoring, "", MMseqsParameter::COMMAND_ALIGN | MMseqsParameter::COMMAND_EXPERT),
+ PARAM_FILTER_HITS(PARAM_FILTER_HITS_ID, "--filter-hits", "Remove hits by seq. id. and coverage", "Filter hits by seq.id. and coverage", typeid(bool), (void *) &filterHits, "", MMseqsParameter::COMMAND_EXPERT),
+ PARAM_SORT_RESULTS(PARAM_SORT_RESULTS_ID, "--sort-results", "Sort results", "Sort results: 0: no sorting, 1: sort by E-value (Alignment) or seq.id. (Hamming)", typeid(int), (void *) &sortResults, "^[0-1]{1}$", MMseqsParameter::COMMAND_EXPERT),
+@@ -130,8 +130,8 @@
+ PARAM_KMER_PER_SEQ(PARAM_KMER_PER_SEQ_ID, "--kmer-per-seq", "k-mers per sequence", "k-mers per sequence", typeid(int), (void *) &kmersPerSequence, "^[1-9]{1}[0-9]*$", MMseqsParameter::COMMAND_CLUSTLINEAR),
+ PARAM_KMER_PER_SEQ_SCALE(PARAM_KMER_PER_SEQ_SCALE_ID, "--kmer-per-seq-scale", "Scale k-mers per sequence", "Scale k-mer per sequence based on sequence length as kmer-per-seq val + scale x seqlen", typeid(MultiParam<float>), (void *) &kmersPerSequenceScale, "^0(\\.[0-9]+)?|1(\\.0+)?$", MMseqsParameter::COMMAND_CLUSTLINEAR),
+ PARAM_INCLUDE_ONLY_EXTENDABLE(PARAM_INCLUDE_ONLY_EXTENDABLE_ID, "--include-only-extendable", "Include only extendable", "Include only extendable", typeid(bool), (void *) &includeOnlyExtendable, "", MMseqsParameter::COMMAND_CLUSTLINEAR),
+- PARAM_IGNORE_MULTI_KMER(PARAM_IGNORE_MULTI_KMER_ID, "--ignore-multi-kmer", "Skip repeating k-mers", "Skip k-mers occuring multiple times (>=2)", typeid(bool), (void *) &ignoreMultiKmer, "", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),
+- PARAM_HASH_SHIFT(PARAM_HASH_SHIFT_ID, "--hash-shift", "Shift hash", "Shift k-mer hash initilization", typeid(int), (void *) &hashShift, "^[1-9]{1}[0-9]*$", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),
++ PARAM_IGNORE_MULTI_KMER(PARAM_IGNORE_MULTI_KMER_ID, "--ignore-multi-kmer", "Skip repeating k-mers", "Skip k-mers occurring multiple times (>=2)", typeid(bool), (void *) &ignoreMultiKmer, "", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),
++ PARAM_HASH_SHIFT(PARAM_HASH_SHIFT_ID, "--hash-shift", "Shift hash", "Shift k-mer hash initialization", typeid(int), (void *) &hashShift, "^[1-9]{1}[0-9]*$", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),
+ PARAM_PICK_N_SIMILAR(PARAM_PICK_N_SIMILAR_ID, "--pick-n-sim-kmer", "Add N similar to search", "Add N similar k-mers to search", typeid(int), (void *) &pickNbest, "^[1-9]{1}[0-9]*$", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),
+ PARAM_ADJUST_KMER_LEN(PARAM_ADJUST_KMER_LEN_ID, "--adjust-kmer-len", "Adjust k-mer length", "Adjust k-mer length based on specificity (only for nucleotides)", typeid(bool), (void *) &adjustKmerLength, "", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),
+ PARAM_RESULT_DIRECTION(PARAM_RESULT_DIRECTION_ID, "--result-direction", "Result direction", "result is 0: query, 1: target centric", typeid(int), (void *) &resultDirection, "^[0-1]{1}$", MMseqsParameter::COMMAND_CLUSTLINEAR | MMseqsParameter::COMMAND_EXPERT),
+@@ -155,9 +155,9 @@
+ PARAM_CONTIG_START_MODE(PARAM_CONTIG_START_MODE_ID, "--contig-start-mode", "Contig start mode", "Contig start can be 0: incomplete, 1: complete, 2: both", typeid(int), (void *) &contigStartMode, "^[0-2]{1}"),
+ PARAM_CONTIG_END_MODE(PARAM_CONTIG_END_MODE_ID, "--contig-end-mode", "Contig end mode", "Contig end can be 0: incomplete, 1: complete, 2: both", typeid(int), (void *) &contigEndMode, "^[0-2]{1}"),
+ PARAM_ORF_START_MODE(PARAM_ORF_START_MODE_ID, "--orf-start-mode", "Orf start mode", "Orf fragment can be 0: from start to stop, 1: from any to stop, 2: from last encountered start to stop (no start in the middle)", typeid(int), (void *) &orfStartMode, "^[0-2]{1}"),
+- PARAM_ORF_FORWARD_FRAMES(PARAM_ORF_FORWARD_FRAMES_ID, "--forward-frames", "Forward frames", "Comma-seperated list of frames on the forward strand to be extracted", typeid(std::string), (void *) &forwardFrames, ""),
+- PARAM_ORF_REVERSE_FRAMES(PARAM_ORF_REVERSE_FRAMES_ID, "--reverse-frames", "Reverse frames", "Comma-seperated list of frames on the reverse strand to be extracted", typeid(std::string), (void *) &reverseFrames, ""),
+- PARAM_USE_ALL_TABLE_STARTS(PARAM_USE_ALL_TABLE_STARTS_ID, "--use-all-table-starts", "Use all table starts", "Use all alteratives for a start codon in the genetic table, if false - only ATG (AUG)", typeid(bool), (void *) &useAllTableStarts, ""),
++ PARAM_ORF_FORWARD_FRAMES(PARAM_ORF_FORWARD_FRAMES_ID, "--forward-frames", "Forward frames", "Comma-separated list of frames on the forward strand to be extracted", typeid(std::string), (void *) &forwardFrames, ""),
++ PARAM_ORF_REVERSE_FRAMES(PARAM_ORF_REVERSE_FRAMES_ID, "--reverse-frames", "Reverse frames", "Comma-separated list of frames on the reverse strand to be extracted", typeid(std::string), (void *) &reverseFrames, ""),
++ PARAM_USE_ALL_TABLE_STARTS(PARAM_USE_ALL_TABLE_STARTS_ID, "--use-all-table-starts", "Use all table starts", "Use all alternatives for a start codon in the genetic table, if false - only ATG (AUG)", typeid(bool), (void *) &useAllTableStarts, ""),
+ PARAM_TRANSLATE(PARAM_TRANSLATE_ID, "--translate", "Translate orf", "Translate ORF to amino acid", typeid(int), (void *) &translate, "^[0-1]{1}"),
+ PARAM_CREATE_LOOKUP(PARAM_CREATE_LOOKUP_ID, "--create-lookup", "Create lookup", "Create database lookup file (can be very large)", typeid(int), (void *) &createLookup, "^[0-1]{1}", MMseqsParameter::COMMAND_EXPERT),
+ // indexdb
+@@ -233,7 +233,7 @@
+ // filtertaxdb
+ PARAM_TAXON_LIST(PARAM_TAXON_LIST_ID, "--taxon-list", "Selected taxa", "Taxonomy ID, possibly multiple values separated by ','", typeid(std::string), (void *) &taxonList, ""),
+ // view
+- PARAM_ID_LIST(PARAM_ID_LIST_ID, "--id-list", "Selected entries with key", "Entries to be printed seperated by ','", typeid(std::string), (void *) &idList, ""),
++ PARAM_ID_LIST(PARAM_ID_LIST_ID, "--id-list", "Selected entries with key", "Entries to be printed separated by ','", typeid(std::string), (void *) &idList, ""),
+ PARAM_IDX_ENTRY_TYPE(PARAM_IDX_ENTRY_TYPE_ID, "--idx-entry-type", "Index entry type", "0: sequence, 1: src sequence, 2: header, 3: src header", typeid(int), (void *) &idxEntryType, "^[0-3]{1}$"),
+ // lca and addtaxonomy
+ PARAM_PICK_ID_FROM(PARAM_PICK_ID_FROM_ID, "--pick-id-from", "Extract mode", "Query 1, Target 2", typeid(int), (void *) &pickIdFrom, "^[1-2]{1}$"),
+@@ -247,9 +247,9 @@
+ PARAM_REPORT_MODE(PARAM_REPORT_MODE_ID, "--report-mode", "Report mode", "Taxonomy report mode 0: Kraken 1: Krona", typeid(int), (void *) &reportMode, "^[0-1]{1}$"),
+ // createtaxdb
+ PARAM_NCBI_TAX_DUMP(PARAM_NCBI_TAX_DUMP_ID, "--ncbi-tax-dump", "NCBI tax dump directory", "NCBI tax dump directory. The tax dump can be downloaded here \"ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz\"", typeid(std::string), (void *) &ncbiTaxDump, ""),
+- PARAM_TAX_MAPPING_FILE(PARAM_TAX_MAPPING_FILE_ID, "--tax-mapping-file", "Taxonomical mapping file", "File to map sequence identifer to taxonomical identifier", typeid(std::string), (void *) &taxMappingFile, ""),
++ PARAM_TAX_MAPPING_FILE(PARAM_TAX_MAPPING_FILE_ID, "--tax-mapping-file", "Taxonomical mapping file", "File to map sequence identifier to taxonomical identifier", typeid(std::string), (void *) &taxMappingFile, ""),
+ // expandaln
+- PARAM_EXPANSION_MODE(PARAM_EXPANSION_MODE_ID, "--expansion-mode", "Expansion mode", "Update score, E-value, and sequence identity by 0: input alignment 1: rescoring the infered backtrace", typeid(int), (void *) &expansionMode, "^[0-2]{1}$"),
++ PARAM_EXPANSION_MODE(PARAM_EXPANSION_MODE_ID, "--expansion-mode", "Expansion mode", "Update score, E-value, and sequence identity by 0: input alignment 1: rescoring the inferred backtrace", typeid(int), (void *) &expansionMode, "^[0-2]{1}$"),
+ // taxonomy
+ PARAM_LCA_MODE(PARAM_LCA_MODE_ID, "--lca-mode", "LCA mode", "LCA Mode 1: Single Search LCA , 2: 2bLCA, 3: approx. 2bLCA, 4: top hit", typeid(int), (void *) &taxonomySearchMode, "^[1-4]{1}$"),
+ PARAM_TAX_OUTPUT_MODE(PARAM_TAX_OUTPUT_MODE_ID, "--tax-output-mode", "Taxonomy output mode", "0: output LCA, 1: output alignment 2: output both", typeid(int), (void *) &taxonomyOutpuMode, "^[0-2]{1}$"),
+--- mmseqs2.orig/src/commons/ProfileStates.cpp
++++ mmseqs2/src/commons/ProfileStates.cpp
+@@ -120,7 +120,7 @@
+
+ if (nalph != 20)
+ {
+- Debug(Debug::WARNING) << "Alphabet size of serialized context profile should be " << 20 << " but is acutally "<< nalph <<"!\n";
++ Debug(Debug::WARNING) << "Alphabet size of serialized context profile should be " << 20 << " but is actually "<< nalph <<"!\n";
+ return -1;
+ }
+
+--- mmseqs2.orig/src/taxonomy/aggregatetax.cpp
++++ mmseqs2/src/taxonomy/aggregatetax.cpp
+@@ -227,7 +227,7 @@
+ outDbStr = par.db5;
+ outDbIndexStr = par.db5Index;
+ } else if (par.voteMode == Parameters::AGG_TAX_MINUS_LOG_EVAL) {
+- Debug(Debug::ERROR) << "voteMode is evalue-based but no alignment databse was provided. consider calling aggregatetaxweights\n";
++ Debug(Debug::ERROR) << "voteMode is evalue-based but no alignment database was provided. consider calling aggregatetaxweights\n";
+ EXIT(EXIT_FAILURE);
+ }
+
=====================================
debian/rules
=====================================
@@ -23,12 +23,12 @@ i386_SIMD_LEVELS=sse2 sse
override_dh_auto_configure-arch:
ifneq (,$(filter $(DEB_HOST_ARCH),amd64 i386))
$(foreach SIMD,$(AMD64_SIMD_LEVELS),export CXXFLAGS="$(CXXFLAGS) -m$(SIMD)" && export CFLAGS="$(CFLAGS) -m$(SIMD)" && \
- dh_auto_configure --builddirectory build_$(SIMD) -- -DEXE_SUFFIX=-$(SIMD) -DVERSION_OVERRIDE=$(DEB_VERSION) -DNATIVE_ARCH=0; )
+ dh_auto_configure --builddirectory build_$(SIMD) -- -DEXE_SUFFIX=-$(SIMD) -DVERSION_OVERRIDE=$(DEB_VERSION) -DNATIVE_ARCH=0 && ) true
export CXXFLAGS="$(CXXFLAGS)" && export CFLAGS="$(CFLAGS)" && \
dh_auto_configure --builddirectory build_plain -- -DEXE_SUFFIX=-plain -DVERSION_OVERRIDE=$(DEB_VERSION) -DNATIVE_ARCH=0
ifeq (i386,$(DEB_HOST_ARCH))
$(foreach SIMD,$(i386_SIMD_LEVELS),export CXXFLAGS="$(CXXFLAGS) -m$(SIMD)" && export CFLAGS="$(CFLAGS) -m$(SIMD)" && \
- dh_auto_configure --builddirectory build_$(SIMD) -- -DEXE_SUFFIX=-$(SIMD) -DVERSION_OVERRIDE=$(DEB_VERSION) -DNATIVE_ARCH=0; )
+ dh_auto_configure --builddirectory build_$(SIMD) -- -DEXE_SUFFIX=-$(SIMD) -DVERSION_OVERRIDE=$(DEB_VERSION) -DNATIVE_ARCH=0 && ) true
endif
else
dh_auto_configure -- -DVERSION_OVERRIDE=$(DEB_VERSION)
@@ -39,9 +39,9 @@ override_dh_auto_configure-indep:
override_dh_auto_build-arch:
ifneq (,$(filter $(DEB_HOST_ARCH),amd64 i386))
mkdir -p $(binprefix)
- $(foreach SIMD,$(AMD64_SIMD_LEVELS),dh_auto_build --builddirectory build_$(SIMD))
+ $(foreach SIMD,$(AMD64_SIMD_LEVELS),dh_auto_build --builddirectory build_$(SIMD) && ) true
ifeq (i386,$(DEB_HOST_ARCH))
- $(foreach SIMD,$(i386_SIMD_LEVELS),dh_auto_build --builddirectory build_$(SIMD))
+ $(foreach SIMD,$(i386_SIMD_LEVELS),dh_auto_build --builddirectory build_$(SIMD) && ) true
endif
else
dh_auto_build
@@ -52,9 +52,9 @@ override_dh_auto_build-indep:
override_dh_auto_install-arch:
ifneq (,$(filter $(DEB_HOST_ARCH),amd64 i386))
dh_install -pmmseqs2 debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/
- $(foreach SIMD,$(AMD64_SIMD_LEVELS),dh_auto_install --builddirectory build_$(SIMD) )
+ $(foreach SIMD,$(AMD64_SIMD_LEVELS),dh_auto_install --builddirectory build_$(SIMD) && ) true
ifeq (i386,$(DEB_HOST_ARCH))
- $(foreach SIMD,$(i386_SIMD_LEVELS),dh_auto_install --builddirectory build_$(SIMD) )
+ $(foreach SIMD,$(i386_SIMD_LEVELS),dh_auto_install --builddirectory build_$(SIMD) && ) true
endif
dh_install -pmmseqs2 usr/bin/mmseqs-* usr/bin/
set -e && cd $(binprefix) \
View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/-/compare/7927390603351bc43634d32e1a36e594db33b510...6f59a6b879afe8071973c7f3667dba253888dfa7
--
View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/-/compare/7927390603351bc43634d32e1a36e594db33b510...6f59a6b879afe8071973c7f3667dba253888dfa7
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