minimap2: harden binaries and add libs to package (#192)

BioArchLinux/minimap2/PKGBUILD

@@ -3,23 +3,44 @@
 
 pkgname=minimap2
 pkgver=2.26
-pkgrel=1
+pkgrel=2
 pkgdesc='A versatile pairwise aligner for genomic and spliced nucleotide sequences. https://doi.org/10.1093/bioinformatics/bty191'
 arch=('x86_64')
 url="https://github.com/lh3/${pkgname}"
 license=('MIT')
-depends=(zlib)
+depends=('zlib' 'glibc')
-provides=()
+provides=('minimap2-lite' 'sdust' 'libminimap2.so')
-source=("${pkgver}.tar.gz::$url/archive/refs/tags/v$pkgver.tar.gz")
+source=("${pkgname}-${pkgver}.tar.gz::$url/archive/refs/tags/v$pkgver.tar.gz"
-sha256sums=('f4c8c3459c7b87e9de6cbed7de019b48d9337c2e46b87ba81b9f72d889420b3c')
+        "hardening.patch")
+sha256sums=('f4c8c3459c7b87e9de6cbed7de019b48d9337c2e46b87ba81b9f72d889420b3c'
+            'ff10a6b715db2e08add52b371842778f855cb4edc9f7fc373c6e1b670ef1415f')
+
+prepare() {
+  cd "${pkgname}-${pkgver}"
+  # Add hardening flags for binaries
+  patch -p1 < "${srcdir}"/hardening.patch
+}
+
 build() {
   cd "${pkgname}-${pkgver}"
-  make
+  # Build all binaries
+  make extra
+
 }
 
 package() {
   cd "${pkgname}-${pkgver}"
-  install -Dm644 LICENSE.txt "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
+  install -Dm644 LICENSE.txt "${pkgdir}"/usr/share/licenses/${pkgname}/LICENSE
-  install -Dm644 ${pkgname} "${pkgdir}/usr/bin/${pkgname}"
+  install -Dm755 libminimap2.so "${pkgdir}"/usr/lib/libminimap2.so
-  chmod +x "${pkgdir}/usr/bin/${pkgname}"
+  install -Dm755 ${pkgname} "${pkgdir}"/usr/bin/${pkgname}
+  install -Dm755 minimap2-lite "${pkgdir}"/usr/bin/minimap2-lite
+  install -Dm755 sdust "${pkgdir}"/usr/bin/sdust
+  # install Manpages
+  install -Dm644 -t "$pkgdir/usr/share/man/man1" minimap2.1
+  # install test Data
+  install -d "${pkgdir}"/usr/share/${pkgname}/test
+  cd test
+  for file in *; do
+    install -Dm644 "$file" "${pkgdir}"/usr/share/${pkgname}/test/"${file}"
+  done
 }

BioArchLinux/minimap2/hardening.patch

@@ -0,0 +1,45 @@
+--- minimap2-2.26.orig/Makefile	2023-04-29 21:51:09.000000000 +0530
++++ minimap2-2.26.new/Makefile	2023-10-21 16:56:41.816040016 +0530
+@@ -1,5 +1,6 @@
+-CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
+-CPPFLAGS=	-DHAVE_KALLOC
++CFLAGS+=		-g -Wall -fPIC -pie -O2 -Wc++-compat #-Wextra
++CPPFLAGS+=	-DHAVE_KALLOC
++LDFLAGS += -pie
+ INCLUDES=
+ OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o \
+ 			lchain.o align.o hit.o seed.o map.o format.o pe.o esterr.o splitidx.o \
+@@ -40,6 +41,8 @@
+ 
+ .PHONY:all extra clean depend
+ .SUFFIXES:.c .o
++NAME := minimap2
++LIBRARY := lib$(NAME).so
+ 
+ .c.o:
+ 		$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
+@@ -48,17 +51,17 @@
+ 
+ extra:all $(PROG_EXTRA)
+ 
+-minimap2:main.o libminimap2.a
+-		$(CC) $(CFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS)
++$(LIBRARY): $(OBJS)
++		$(CC) $(LDFLAGS) -shared -Wl,-soname,lib$(NAME).so $^ -lm -lz -o $@
+ 
+-minimap2-lite:example.o libminimap2.a
+-		$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
++minimap2:main.o libminimap2.so
++		$(CC) $(LDFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS)
+ 
+-libminimap2.a:$(OBJS)
+-		$(AR) -csru $@ $(OBJS)
++minimap2-lite:example.o libminimap2.so
++		$(CC) $(LDFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
+ 
+ sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h
+-		$(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz
++		$(CC) $(LDFLAGS) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz
+ 
+ # SSE-specific targets on x86/x86_64
+ 

BioArchLinux/minimap2/lilac.yaml

@@ -12,3 +12,8 @@ update_on:
     github: lh3/minimap2
     use_max_tag: true
     prefix: 'v'
+  - source: alpm
+    alpm: zlib
+    repo: core
+    provided: libz.so
+    strip_release: true