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kraken2: build fix for version 2.1.4

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kbipinkumar 2025-02-20 12:25:04 +05:30
parent 8f884b7a8c
commit ca1fc88824
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GPG key ID: C67233497C15E476
2 changed files with 29 additions and 28 deletions
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32
BioArchLinux/kraken2/Makefile.patch
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@ -1,7 +1,7 @@
--- kraken2-2.1.3.orig/src/Makefile 2023-06-07 05:55:37.000000000 +0530 --- kraken2-2.14/src/Makefile 2025-02-18 09:29:30.000000000 +0530
+++ kraken2-2.1.3.new/src/Makefile 2023-06-07 15:11:05.404521211 +0530 +++ kraken2-2.14.new/src/Makefile 2025-02-19 22:39:05.587331135 +0530
@@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
CXX = g++ CXX ?= g++
KRAKEN2_SKIP_FOPENMP ?= -fopenmp KRAKEN2_SKIP_FOPENMP ?= -fopenmp
-CXXFLAGS = $(KRAKEN2_SKIP_FOPENMP) -Wall -std=c++11 -O3 -CXXFLAGS = $(KRAKEN2_SKIP_FOPENMP) -Wall -std=c++11 -O3
+CXXFLAGS = $(KRAKEN2_SKIP_FOPENMP) -Wall -std=c++11 -O2 +CXXFLAGS = $(KRAKEN2_SKIP_FOPENMP) -Wall -std=c++11 -O2
@ -13,7 +13,7 @@
install: $(PROGS) install: $(PROGS)
- cp $(PROGS) "$(KRAKEN2_DIR)/" - cp $(PROGS) "$(KRAKEN2_DIR)/"
+ cp $(PROGS) $(DESTDIR)$(KRAKEN2_DIR)/ + cp $(PROGS) $(DESTDIR)"$(KRAKEN2_DIR)/"
clean: clean:
rm -f *.o $(PROGS) rm -f *.o $(PROGS)
@ -21,25 +21,25 @@
k2mask.o: k2mask.cc gzstream.h threadpool.h k2mask.o: k2mask.cc gzstream.h threadpool.h
build_db: build_db.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o utilities.o build_db: build_db.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o utilities.o
- $(CXX) $(CXXFLAGS) -o $@ $^ - $(CXX) $(CXXFLAGS) -o $@ build_db.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o utilities.o
+ $(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS) + $(CXX) $(CXXFLAGS) -o $@ $(LDFLAGS) build_db.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o utilities.o
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 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
- $(CXX) $(CXXFLAGS) -o $@ $^ - $(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
+ $(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS) + $(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
estimate_capacity: estimate_capacity.o seqreader.o mmscanner.o omp_hack.o utilities.o estimate_capacity: estimate_capacity.o seqreader.o mmscanner.o omp_hack.o utilities.o
- $(CXX) $(CXXFLAGS) -o $@ $^ - $(CXX) $(CXXFLAGS) -o $@ estimate_capacity.o seqreader.o mmscanner.o omp_hack.o utilities.o
+ $(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS) + $(CXX) $(CXXFLAGS) -o $@ $(LDFLAGS) estimate_capacity.o seqreader.o mmscanner.o omp_hack.o utilities.o
dump_table: dump_table.o mmap_file.o compact_hash.o omp_hack.o taxonomy.o reports.o hyperloglogplus.o dump_table: dump_table.o mmap_file.o compact_hash.o omp_hack.o taxonomy.o reports.o hyperloglogplus.o
- $(CXX) $(CXXFLAGS) -o $@ $^ - $(CXX) $(CXXFLAGS) -o $@ dump_table.o mmap_file.o compact_hash.o omp_hack.o taxonomy.o reports.o hyperloglogplus.o
+ $(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS) + $(CXX) $(CXXFLAGS) -o $@ $(LDFLAGS) dump_table.o mmap_file.o compact_hash.o omp_hack.o taxonomy.o reports.o hyperloglogplus.o
lookup_accession_numbers: lookup_accession_numbers.o mmap_file.o omp_hack.o utilities.o lookup_accession_numbers: lookup_accession_numbers.o mmap_file.o omp_hack.o utilities.o
- $(CXX) $(CXXFLAGS) -o $@ $^ - $(CXX) $(CXXFLAGS) -o $@ lookup_accession_numbers.o mmap_file.o omp_hack.o utilities.o
+ $(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS) + $(CXX) $(CXXFLAGS) -o $@ $(LDFLAGS) lookup_accession_numbers.o mmap_file.o omp_hack.o utilities.o
k2mask: k2mask.o seqreader.o k2mask: k2mask.o seqreader.o
- $(CXX) $(CXXFLAGS) -o $@ $^ -lz -pthread - $(CXX) $(CXXFLAGS) -o $@ k2mask.o seqreader.o -lz -pthread
+ $(CXX) $(CXXFLAGS) -o $@ $^ -lz -pthread $(LDFLAGS) + $(CXX) $(CXXFLAGS) -o $@ $(LDFLAGS) k2mask.o seqreader.o -lz -pthread

25
BioArchLinux/kraken2/PKGBUILD
View file

@ -1,38 +1,39 @@
pkgname=kraken2 pkgname=kraken2
pkgver=2.1.3 pkgver=2.1.4
pkgrel=1 _pkgver=$(echo "$pkgver" | sed 's/\.//2')
pkgrel=0
pkgdesc="Improved vesion of kraken ultrafast metagenomic sequence classification tool. https://doi.org/10.1186/s13059-019-1891-0" pkgdesc="Improved vesion of kraken ultrafast metagenomic sequence classification tool. https://doi.org/10.1186/s13059-019-1891-0"
arch=('i686' 'x86_64') arch=('i686' 'x86_64')
url="https://github.com/DerrickWood/kraken2" url="https://github.com/DerrickWood/kraken2"
license=('MIT') license=('MIT')
depends=('glibc' 'gcc-libs' 'blast+' 'perl' 'bash' 'python' 'zlib') depends=('glibc' 'gcc-libs' 'blast+' 'perl' 'bash' 'python' 'zlib')
source=("${pkgname}-${pkgver}.tar.gz::https://github.com/DerrickWood/kraken2/archive/refs/tags/v${pkgver}.tar.gz" source=("${pkgname}-${pkgver}.tar.gz::https://github.com/DerrickWood/kraken2/archive/refs/tags/v${_pkgver}.tar.gz"
'Makefile.patch' 'Makefile.patch'
'fastaread.patch') 'fastaread.patch')
sha256sums=('5269fa14adfb02e38c2da2e605e909a432d76c680d73e2e0e80e27ccd04d7c69' sha256sums=('75ffbf82bd13232ec8d39990f48454c6f7d98ceb589af80a60c7e9ed046e7f18'
'e57d358f4cc234831bf7808bb72a423ebbe13feefeba7204cd2b82fa6f3ea09b' 'e08f748b3e34ec5efd05756886e8b8901ff5710f8ea67927e2666166c3e7d9ca'
'40bdae9d36e7212197f32d5dc49d7d676593e0a0e0f51e7ef8c0c20ccd2d999e') '40bdae9d36e7212197f32d5dc49d7d676593e0a0e0f51e7ef8c0c20ccd2d999e')
prepare() { prepare() {
cp Makefile.patch ${pkgname}-${pkgver}/src cp Makefile.patch ${pkgname}-${_pkgver}/
cp fastaread.patch ${pkgname}-${pkgver}/scripts cp fastaread.patch ${pkgname}-${_pkgver}/scripts
cd ${pkgname}-${pkgver}/src cd ${pkgname}-${_pkgver}
# patch makefile to use $(DESTDIR) and LDFLAGS # patch makefile to use $(DESTDIR) and LDFLAGS
patch -p2 < Makefile.patch patch -p1 < Makefile.patch
cd ../scripts cd scripts/
# Slighly more robust method to obtain taxid of fasta files # Slighly more robust method to obtain taxid of fasta files
patch -p1 < fastaread.patch patch -p1 < fastaread.patch
} }
build() { build() {
cd ${pkgname}-${pkgver}/src cd ${pkgname}-${_pkgver}/src
export KRAKEN2_DIR=/usr/lib/kraken2 export KRAKEN2_DIR=/usr/lib/kraken2
make make
} }
package() { package() {
cd ${pkgname}-${pkgver}/src cd ${pkgname}-${_pkgver}/src
install -d ${pkgdir}/usr/bin install -d ${pkgdir}/usr/bin
install -d ${pkgdir}/usr/lib/kraken2 install -d ${pkgdir}/usr/lib/kraken2
install -d ${pkgdir}/usr/share/${pkgname} install -d ${pkgdir}/usr/share/${pkgname}