allelecount: add version 4.3.0

BioArchLinux/allelecount/PKGBUILD

@@ -0,0 +1,38 @@
+# Maintainer: Bipin Kumar <kbipinkumar@pm.me>
+
+pkgname=allelecount
+_pkgname=alleleCount
+pkgver=4.3.0
+pkgrel=1
+pkgdesc="program for estimating the NGS copy number" 
+arch=('x86_64')
+url="http://cancerit.github.io/alleleCount/"
+license=('AGPL3')
+depends=('glibc' 'htslib' 'bzip2' 'xz' 'zlib')
+makedepends=('quilt' 'perl')
+source=("${pkgname}-${pkgver}.tar.gz::https://github.com/cancerit/alleleCount/archive/refs/tags/v${pkgver}.tar.gz"
+		'series'
+		'harden.patch')
+b2sums=('f0f2077d0efed1a9f4db76648ae375ea30989909d255917b5b280e32187a27aaf1e1844bccae8b659c34081d34592d3782b7d6df926ece79dcea62cb966b4539'
+        '55807c3d06f035d18040248d272bb150bc84ef44c4e01ae984f3abe27fd34d6f18abe5bc1cbb2945435725d2344a5b5209b37ac322cc1ff5fae1612c265c1b9b'
+        '9de3b1c44db6e8b0e2321450d19d741ad233eabb00d32c6f951e78177ee1bd36d150c3685eb7c373f806c694d3c84b94e7e4fd5683387f85587de35a646c7066')
+
+prepare(){
+    mkdir -p ${_pkgname}-${pkgver}/patches
+    cp *.patch ${_pkgname}-${pkgver}/patches
+    cp series ${_pkgname}-${pkgver}/patches
+    # Apply Patches
+    cd ${_pkgname}-${pkgver}/patches
+    quilt push -a
+}
+
+build() {
+	cd ${_pkgname}-${pkgver}/c
+	export HTSLIB=/usr/lib
+	make prefix=/usr
+}
+
+package() {
+	cd ${_pkgname}-${pkgver}/c/bin
+	install -Dm755 alleleCounter ${pkgdir}/usr/bin/alleleCounter
+}

BioArchLinux/allelecount/harden.patch

@@ -0,0 +1,24 @@
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 11 May 2020 16:16:46 +0200
+Description: Propagate hardening flags
+
+--- a/c/Makefile
++++ b/c/Makefile
+@@ -6,7 +6,7 @@ CC = gcc -O3 -DALLELECOUNTER_VERSION='"$
+ #compiler flags
+ # -g adds debug info to the executable file
+ # -Wall turns on most warnings from compiler
+-CFLAGS = -g -Wall
++CFLAGS += -g -Wall
+ 
+ #Location of samtools/htslib libraries
+ HTSLOC?=$(HTSLIB)
+@@ -67,7 +67,7 @@ all: clean make_bin make_htslib_tmp $(CO
+ 	@echo  Binaries have been compiled.
+ 
+ $(COUNTER_TARGET): $(OBJS)
+-	$(CC) $(JOIN_INCLUDES) $(INCLUDES) $(CFLAGS) -o $(COUNTER_TARGET) $(OBJS) $(LFLAGS) $(CAT_LFLAGS) $(LIBS) ./src/alleleCounter.c
++	$(CC) $(JOIN_INCLUDES) $(INCLUDES) $(CFLAGS) -o $(COUNTER_TARGET) $(OBJS) $(LFLAGS) $(CAT_LFLAGS) $(LIBS) ./src/alleleCounter.c $(LDFLAGS)
+ 
+ #Unit Tests
+ test: $(COUNTER_TARGET)

BioArchLinux/allelecount/lilac.yaml

@@ -0,0 +1,17 @@
+maintainers:
+  - github: kbipinkumar
+    email: kbipinkumar@pm.me
+build_prefix: extra-x86_64
+pre_build_script: |
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+  run_cmd(['updpkgsums'])
+post_build_script: |
+  git_pkgbuild_commit()
+  update_aur_repo()
+repo_depends:
+  - htslib
+update_on:
+  - source: github
+    github: cancerit/alleleCount
+    use_max_tag: true
+    prefix: 'v'

BioArchLinux/allelecount/series

@@ -0,0 +1 @@
+harden.patch