amrfinderplus: cleanup PKGBUILD

BioArchLinux/amrfinderplus/PKGBUILD

@@ -1,4 +1,4 @@
-# Maintianer: Bipin Kumar <bipin@ccmb.res.in>
+# Maintianer: Bipin Kumar <kbipinkumar@pm.me>
 
 pkgname=amrfinderplus
 pkgver=3.11.20
@@ -17,7 +17,7 @@ depends=(
 source=("${pkgname}-${pkgver}.tar.gz::https://github.com/ncbi/amr/archive/refs/tags/amrfinder_v${pkgver}.tar.gz"
 		"destdir.patch")
 sha256sums=('698462c4fa688a91130b72e44756d21faf406e186a02da914982044332419ef6'
-            '1364d6dedb96c9a5aa2353e9abe7f766d721f55cb0811dd0aece43639f0f2152')
+            '2adee0fa212d4b45054fdd9be5c31298bef7caa079c46d7c26340cb64375c1e4')
 
 prepare() {
   cp *.patch amr-amrfinder_v${pkgver}
@@ -28,12 +28,14 @@ prepare() {
 
 build() {
     cd amr-amrfinder_v${pkgver}
-    make PREFIX=/usr DEFAULT_DB_DIR=/usr/share/amrfinderplus/data
+    export LDFLAGS="-Wl,-O2,--sort-common,--as-needed,-z,relro,-z,now"
+    export PREFIX="/usr"
+    export DEFAULT_DB_DIR="/usr/share/amrfinderplus/data"
+    make
 }
 
 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
@@ -44,4 +46,4 @@ package() {
      -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 
-}
+}

BioArchLinux/amrfinderplus/destdir.patch

@@ -1,14 +1,5 @@
 --- 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
++++ amr-amrfinder_v3.11.20.new/Makefile	2023-09-24 11:02:41.286592064 +0530
 @@ -73,12 +73,12 @@
    CPPFLAGS = -std=gnu++17 -pthread --signed-char -falign-jumps -fno-math-errno -O3 
  else
@@ -84,9 +75,12 @@
  
  
  
-@@ -154,9 +154,9 @@
+@@ -152,11 +152,11 @@
+ 	rm -f $(BINARIES)
+ 
  install:
- 	@if [ ! -e $(bindir) ]; \
+-	@if [ ! -e $(bindir) ]; \
++	@if [ ! -e $(DESTDIR)$(bindir) ]; \
  	then \
 -		mkdir -p $(bindir); \
 +		mkdir -p $(DESTDIR)$(bindir); \