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kraken2: build fix for version 2.1.4
This commit is contained in:
kbipinkumar
parent
8f884b7a8c
commit
ca1fc88824
2 changed files with 29 additions and 28 deletions
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@ -1,7 +1,7 @@
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--- kraken2-2.1.3.orig/src/Makefile 2023-06-07 05:55:37.000000000 +0530
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+++ kraken2-2.1.3.new/src/Makefile 2023-06-07 15:11:05.404521211 +0530
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--- kraken2-2.14/src/Makefile 2025-02-18 09:29:30.000000000 +0530
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+++ kraken2-2.14.new/src/Makefile 2025-02-19 22:39:05.587331135 +0530
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@@ -1,6 +1,6 @@
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CXX = g++
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CXX ?= g++
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KRAKEN2_SKIP_FOPENMP ?= -fopenmp
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-CXXFLAGS = $(KRAKEN2_SKIP_FOPENMP) -Wall -std=c++11 -O3
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+CXXFLAGS = $(KRAKEN2_SKIP_FOPENMP) -Wall -std=c++11 -O2
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@ -13,7 +13,7 @@
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install: $(PROGS)
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- cp $(PROGS) "$(KRAKEN2_DIR)/"
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+ cp $(PROGS) $(DESTDIR)$(KRAKEN2_DIR)/
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+ cp $(PROGS) $(DESTDIR)"$(KRAKEN2_DIR)/"
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clean:
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rm -f *.o $(PROGS)
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@ -21,25 +21,25 @@
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k2mask.o: k2mask.cc gzstream.h threadpool.h
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build_db: build_db.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o utilities.o
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- $(CXX) $(CXXFLAGS) -o $@ $^
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+ $(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS)
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- $(CXX) $(CXXFLAGS) -o $@ build_db.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o utilities.o
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+ $(CXX) $(CXXFLAGS) -o $@ $(LDFLAGS) build_db.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o utilities.o
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classify: classify.o reports.o hyperloglogplus.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o aa_translate.o utilities.o
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- $(CXX) $(CXXFLAGS) -o $@ $^
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+ $(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS)
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- $(CXX) $(CXXFLAGS) -o $@ classify.o reports.o hyperloglogplus.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o aa_translate.o utilities.o
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+ $(CXX) $(CXXFLAGS) -o $@ $(LDFLAGS) classify.o reports.o hyperloglogplus.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o aa_translate.o utilities.o
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estimate_capacity: estimate_capacity.o seqreader.o mmscanner.o omp_hack.o utilities.o
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- $(CXX) $(CXXFLAGS) -o $@ $^
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+ $(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS)
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- $(CXX) $(CXXFLAGS) -o $@ estimate_capacity.o seqreader.o mmscanner.o omp_hack.o utilities.o
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+ $(CXX) $(CXXFLAGS) -o $@ $(LDFLAGS) estimate_capacity.o seqreader.o mmscanner.o omp_hack.o utilities.o
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dump_table: dump_table.o mmap_file.o compact_hash.o omp_hack.o taxonomy.o reports.o hyperloglogplus.o
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- $(CXX) $(CXXFLAGS) -o $@ $^
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+ $(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS)
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- $(CXX) $(CXXFLAGS) -o $@ dump_table.o mmap_file.o compact_hash.o omp_hack.o taxonomy.o reports.o hyperloglogplus.o
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+ $(CXX) $(CXXFLAGS) -o $@ $(LDFLAGS) dump_table.o mmap_file.o compact_hash.o omp_hack.o taxonomy.o reports.o hyperloglogplus.o
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lookup_accession_numbers: lookup_accession_numbers.o mmap_file.o omp_hack.o utilities.o
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- $(CXX) $(CXXFLAGS) -o $@ $^
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+ $(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS)
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- $(CXX) $(CXXFLAGS) -o $@ lookup_accession_numbers.o mmap_file.o omp_hack.o utilities.o
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+ $(CXX) $(CXXFLAGS) -o $@ $(LDFLAGS) lookup_accession_numbers.o mmap_file.o omp_hack.o utilities.o
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k2mask: k2mask.o seqreader.o
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- $(CXX) $(CXXFLAGS) -o $@ $^ -lz -pthread
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+ $(CXX) $(CXXFLAGS) -o $@ $^ -lz -pthread $(LDFLAGS)
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- $(CXX) $(CXXFLAGS) -o $@ k2mask.o seqreader.o -lz -pthread
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+ $(CXX) $(CXXFLAGS) -o $@ $(LDFLAGS) k2mask.o seqreader.o -lz -pthread
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@ -1,38 +1,39 @@
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pkgname=kraken2
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pkgver=2.1.3
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pkgrel=1
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pkgver=2.1.4
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_pkgver=$(echo "$pkgver" | sed 's/\.//2')
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pkgrel=0
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pkgdesc="Improved vesion of kraken ultrafast metagenomic sequence classification tool. https://doi.org/10.1186/s13059-019-1891-0"
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arch=('i686' 'x86_64')
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url="https://github.com/DerrickWood/kraken2"
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license=('MIT')
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depends=('glibc' 'gcc-libs' 'blast+' 'perl' 'bash' 'python' 'zlib')
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source=("${pkgname}-${pkgver}.tar.gz::https://github.com/DerrickWood/kraken2/archive/refs/tags/v${pkgver}.tar.gz"
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source=("${pkgname}-${pkgver}.tar.gz::https://github.com/DerrickWood/kraken2/archive/refs/tags/v${_pkgver}.tar.gz"
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'Makefile.patch'
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'fastaread.patch')
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sha256sums=('5269fa14adfb02e38c2da2e605e909a432d76c680d73e2e0e80e27ccd04d7c69'
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'e57d358f4cc234831bf7808bb72a423ebbe13feefeba7204cd2b82fa6f3ea09b'
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sha256sums=('75ffbf82bd13232ec8d39990f48454c6f7d98ceb589af80a60c7e9ed046e7f18'
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'e08f748b3e34ec5efd05756886e8b8901ff5710f8ea67927e2666166c3e7d9ca'
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'40bdae9d36e7212197f32d5dc49d7d676593e0a0e0f51e7ef8c0c20ccd2d999e')
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prepare() {
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cp Makefile.patch ${pkgname}-${pkgver}/src
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cp fastaread.patch ${pkgname}-${pkgver}/scripts
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cd ${pkgname}-${pkgver}/src
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cp Makefile.patch ${pkgname}-${_pkgver}/
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cp fastaread.patch ${pkgname}-${_pkgver}/scripts
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cd ${pkgname}-${_pkgver}
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# patch makefile to use $(DESTDIR) and LDFLAGS
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patch -p2 < Makefile.patch
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cd ../scripts
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patch -p1 < Makefile.patch
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cd scripts/
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# Slighly more robust method to obtain taxid of fasta files
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patch -p1 < fastaread.patch
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}
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build() {
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cd ${pkgname}-${pkgver}/src
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cd ${pkgname}-${_pkgver}/src
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export KRAKEN2_DIR=/usr/lib/kraken2
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make
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}
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package() {
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cd ${pkgname}-${pkgver}/src
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cd ${pkgname}-${_pkgver}/src
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install -d ${pkgdir}/usr/bin
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install -d ${pkgdir}/usr/lib/kraken2
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install -d ${pkgdir}/usr/share/${pkgname}
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