amrfinderplus: updated to 3.11.20

3 files changed, 164 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..ddf9ebf3f8b2
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,19 @@
+pkgbase = amrfinderplus
+	pkgdesc = Identify Antimicrobial resistance genes in assembled bacterial nucleotide and protein sequence. https://doi.org/10.1038/s41598-021-91456-0
+	pkgver = 3.11.20
+	pkgrel = 1
+	url = https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/
+	arch = x86_64
+	arch = i686
+	license = custom: Public Domain
+	depends = glibc
+	depends = gcc-libs
+	depends = curl
+	depends = blast+
+	depends = hmmer
+	source = amrfinderplus-3.11.20.tar.gz::https://github.com/ncbi/amr/archive/refs/tags/amrfinder_v3.11.20.tar.gz
+	source = destdir.patch
+	sha256sums = 698462c4fa688a91130b72e44756d21faf406e186a02da914982044332419ef6
+	sha256sums = 1364d6dedb96c9a5aa2353e9abe7f766d721f55cb0811dd0aece43639f0f2152
+
+pkgname = amrfinderplus
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..1050f28a1bcf
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,47 @@
+# Maintianer: Bipin Kumar <bipin@ccmb.res.in>
+
+pkgname=amrfinderplus
+pkgver=3.11.20
+pkgrel=1
+pkgdesc="Identify Antimicrobial resistance genes in assembled bacterial nucleotide and protein sequence. https://doi.org/10.1038/s41598-021-91456-0"
+arch=('x86_64' 'i686')
+url="https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/"
+license=('custom: Public Domain')
+depends=(
+        'glibc'
+        'gcc-libs'
+        'curl'
+        'blast+'
+        'hmmer'
+        )
+source=("${pkgname}-${pkgver}.tar.gz::https://github.com/ncbi/amr/archive/refs/tags/amrfinder_v${pkgver}.tar.gz"
+		"destdir.patch")
+sha256sums=('698462c4fa688a91130b72e44756d21faf406e186a02da914982044332419ef6'
+            '1364d6dedb96c9a5aa2353e9abe7f766d721f55cb0811dd0aece43639f0f2152')
+
+prepare() {
+  cp *.patch amr-amrfinder_v${pkgver}
+  cd amr-amrfinder_v${pkgver}
+  # patch Makefile to use gnu make's destdir variable
+  patch -p1 < destdir.patch
+}
+
+build() {
+    cd amr-amrfinder_v${pkgver}
+    make PREFIX=/usr DEFAULT_DB_DIR=/usr/share/amrfinderplus/data
+}
+
+package() {
+    cd amr-amrfinder_v${pkgver}
+    install -d ${pkgdir}/usr/bin
+    make DESTDIR=${pkgdir} install
+    install -Dm644 LICENSE  -t "$pkgdir"/usr/share/licenses/"${pkgname}"
+    install -d ${pkgdir}/usr/share/amrfinderplus/data
+    cd ${pkgdir}/usr/share/amrfinderplus/data
+    curl -O https://raw.githubusercontent.com/ncbi/amr/master/test_dna.fa \
+     -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.fa \
+     -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.gff \
+     -O https://raw.githubusercontent.com/ncbi/amr/master/test_both.expected \
+     -O https://raw.githubusercontent.com/ncbi/amr/master/test_dna.expected \
+     -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.expected 
+}
diff --git a/destdir.patch b/destdir.patch
new file mode 100644
index 000000000000..bc77265c215b
--- /dev/null
+++ b/destdir.patch
@@ -0,0 +1,98 @@
+--- amr-amrfinder_v3.11.20.orig/Makefile	2023-09-06 22:49:21.000000000 +0530
++++ amr-amrfinder_v3.11.20.new/Makefile	2023-09-21 00:23:04.406125302 +0530
+@@ -37,7 +37,7 @@
+ # This is a little convoluted because I broke things and don't want
+ # to change two different ways of defining the paths. This could
+ # be simplified in a later release
+-PREFIX ?= /usr/local
++PREFIX ?= /usr
+ ifneq '$(INSTALL_DIR)' ''
+ 	bindir=$(INSTALL_DIR)
+ endif
+@@ -73,12 +73,12 @@
+   CPPFLAGS = -std=gnu++17 -pthread --signed-char -falign-jumps -fno-math-errno -O3 
+ else
+   # set x86_x64 CFLAGS
+-  CPPFLAGS = -std=gnu++17 -pthread -malign-double -fno-math-errno -O3
++  CPPFLAGS = -std=gnu++17 -pthread -malign-double -fno-math-errno -O2
+ endif
+ # was: -std=gnu++14 
+ 
+ CXX=g++
+-COMPILE.cpp= $(CXX) $(CPPFLAGS) $(SVNREV) $(DBDIR) $(TEST_UPDATE_DB) -c 
++COMPILE.cpp= $(CXX) $(CPPFLAGS) $(LDFLAGS) $(SVNREV) $(DBDIR) $(TEST_UPDATE_DB) -c 
+ 
+ 
+ .PHONY: all clean install release 
+@@ -99,12 +99,12 @@
+ amr_report.o:	common.hpp common.inc gff.hpp alignment.hpp
+ amr_reportOBJS=amr_report.o common.o gff.o alignment.o
+ amr_report:	$(amr_reportOBJS)
+-	$(CXX) -o $@ $(amr_reportOBJS)
++	$(CXX) $(LDFLAGS) -o $@ $(amr_reportOBJS)
+ 
+ amrfinder.o:  common.hpp common.inc gff.hpp
+ amrfinderOBJS=amrfinder.o common.o gff.o tsv.o
+ amrfinder:	$(amrfinderOBJS)
+-	$(CXX) -o $@ $(amrfinderOBJS) -pthread $(DBDIR)
++	$(CXX) $(LDFLAGS) -o $@ $(amrfinderOBJS) -pthread $(DBDIR)
+ 
+ amrfinder_update.o:  common.hpp common.inc 
+ amrfinder_updateOBJS=amrfinder_update.o common.o curl_easy.o
+@@ -113,37 +113,37 @@
+ 	then  \
+ 		touch amrfinder_update.cpp ;\
+ 	fi # make sure the next make command rebuilds amrfinder_update
+-	$(CXX) -o $@ $(amrfinder_updateOBJS) -lcurl 
++	$(CXX) $(LDFLAGS) -o $@ $(amrfinder_updateOBJS) -lcurl 
+ 
+ amrfinder_index.o:  common.hpp common.inc 
+ amrfinder_indexOBJS=amrfinder_index.o common.o
+ amrfinder_index:      $(amrfinder_indexOBJS) 
+-	$(CXX) -o $@ $(amrfinder_indexOBJS) 
++	$(CXX) $(LDFLAGS) -o $@ $(amrfinder_indexOBJS) 
+ 
+ fasta_check.o:	common.hpp common.inc 
+ fasta_checkOBJS=fasta_check.o common.o 
+ fasta_check:	$(fasta_checkOBJS)
+-	$(CXX) -o $@ $(fasta_checkOBJS)
++	$(CXX) $(LDFLAGS) -o $@ $(fasta_checkOBJS)
+ 
+ fasta_extract.o:	common.hpp common.inc
+ fasta_extractOBJS=fasta_extract.o common.o
+ fasta_extract:	$(fasta_extractOBJS)
+-	$(CXX) -o $@ $(fasta_extractOBJS)
++	$(CXX) $(LDFLAGS) -o $@ $(fasta_extractOBJS)
+ 
+ fasta2parts.o:	common.hpp common.inc
+ fasta2partsOBJS=fasta2parts.o common.o
+ fasta2parts:	$(fasta2partsOBJS)
+-	$(CXX) -o $@ $(fasta2partsOBJS)
++	$(CXX) $(LDFLAGS) -o $@ $(fasta2partsOBJS)
+ 
+ gff_check.o:	common.hpp common.inc gff.hpp
+ gff_checkOBJS=gff_check.o common.o gff.o
+ gff_check:	$(gff_checkOBJS)
+-	$(CXX) -o $@ $(gff_checkOBJS)
++	$(CXX) $(LDFLAGS) -o $@ $(gff_checkOBJS)
+ 
+ dna_mutation.o:	common.hpp common.inc alignment.hpp
+ dna_mutationOBJS=dna_mutation.o common.o alignment.o
+ dna_mutation:	$(dna_mutationOBJS)
+-	$(CXX) -o $@ $(dna_mutationOBJS)
++	$(CXX) $(LDFLAGS) -o $@ $(dna_mutationOBJS)
+ 
+ 
+ 
+@@ -154,9 +154,9 @@
+ install:
+ 	@if [ ! -e $(bindir) ]; \
+ 	then \
+-		mkdir -p $(bindir); \
++		mkdir -p $(DESTDIR)$(bindir); \
+ 	fi
+-	$(INSTALL) $(BINARIES) $(bindir)
++	$(INSTALL) $(BINARIES) $(DESTDIR)$(bindir)
+ 
+ # amrfinder binaries for github binary release
+ GITHUB_FILE=amrfinder_binaries_v$(VERSION_STRING)