diff options
| author | bipin kumar | 2023-05-09 15:21:05 +0530 |
|---|---|---|
| committer | bipin kumar | 2023-05-09 15:21:05 +0530 |
| commit | 11eae05a54f958e240d9725937a0d59a6c1021c8 (patch) | |
| tree | 59d52964ab0cad9321606f13136ff54b3aa76963 | |
| download | aur-allelecount.tar.gz | |
allelecount: initial upload
| -rw-r--r-- | .SRCINFO | 22 | ||||
| -rw-r--r-- | PKGBUILD | 38 | ||||
| -rw-r--r-- | harden.patch | 24 | ||||
| -rw-r--r-- | series | 1 |
4 files changed, 85 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..40bc34efefde --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,22 @@ +pkgbase = allelecount + pkgdesc = program for estimating the NGS copy number + pkgver = 4.3.0 + pkgrel = 1 + url = http://cancerit.github.io/alleleCount/ + arch = x86_64 + license = AGPL3 + makedepends = quilt + makedepends = perl + depends = glibc + depends = htslib + depends = bzip2 + depends = xz + depends = zlib + source = allelecount-4.3.0.tar.gz::https://github.com/cancerit/alleleCount/archive/refs/tags/v4.3.0.tar.gz + source = series + source = harden.patch + b2sums = f0f2077d0efed1a9f4db76648ae375ea30989909d255917b5b280e32187a27aaf1e1844bccae8b659c34081d34592d3782b7d6df926ece79dcea62cb966b4539 + b2sums = 55807c3d06f035d18040248d272bb150bc84ef44c4e01ae984f3abe27fd34d6f18abe5bc1cbb2945435725d2344a5b5209b37ac322cc1ff5fae1612c265c1b9b + b2sums = 9de3b1c44db6e8b0e2321450d19d741ad233eabb00d32c6f951e78177ee1bd36d150c3685eb7c373f806c694d3c84b94e7e4fd5683387f85587de35a646c7066 + +pkgname = allelecount diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..5ff846dd253c --- /dev/null +++ b/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 ${pkgdir}/usr/bin/alleleCounter +} diff --git a/harden.patch b/harden.patch new file mode 100644 index 000000000000..9a13e5dace0d --- /dev/null +++ b/harden.patch @@ -0,0 +1,24 @@ +Author: Andreas Tille <tille@debian.org> +Last-Update: Mon, 11 May 2020 16:16:46 +0200 +Description: Propagate hardening flags + +--- a/c/Makefile ++++ b/c/Makefile +@@ -6,7 +6,7 @@ CC = gcc -O3 -DALLELECOUNTER_VERSION='"$ + #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)
\ No newline at end of file diff --git a/series b/series new file mode 100644 index 000000000000..a2f2d63243ea --- /dev/null +++ b/series @@ -0,0 +1 @@ +harden.patch
\ No newline at end of file |