add bcftools

bcftools/PKGBUILD

@@ -0,0 +1,32 @@
+# Maintainer:  Andrew O'Neill <andrew at meanjollies dot com>
+# Contributor: Christian Krause ("wookietreiber") <christian.krause@mailbox.org>
+
+pkgname=bcftools
+pkgver=1.14
+pkgrel=1
+pkgdesc='A program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF'
+arch=('x86_64')
+url='https://samtools.github.io/bcftools'
+license=('GPL')
+depends=('gsl' 'htslib' 'python-matplotlib' 'python')
+source=("https://github.com/samtools/${pkgname}/releases/download/${pkgver}/${pkgname}-${pkgver}.tar.bz2")
+sha256sums=('b7ef88ae89fcb55658c5bea2e8cb8e756b055e13860036d6be13756782aa19cb')
+
+build() {
+  cd "${pkgname}-${pkgver}"
+
+  ./configure \
+    --prefix=/usr \
+    --enable-libgsl \
+    --with-bcf-plugin-dir=/usr/lib/${pkgname} \
+    --with-cblas=gslcblas \
+    --with-htslib=system
+
+  make
+}
+
+package() {
+  cd "${pkgname}-${pkgver}"
+
+  make DESTDIR="${pkgdir}" install
+}

bcftools/lilac.py

@@ -0,0 +1,10 @@
+#!/usr/bin/env python3
+
+from lilaclib import *
+
+def pre_build():
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+
+def post_build():
+  git_add_files('PKGBUILD')
+  git_commit()

bcftools/lilac.yaml

@@ -0,0 +1,10 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: starsareintherose@outlook.com
+update_on:
+  - source: github
+    github: samtools/bcftools
+    use_latest_release: true
+repo_depends:
+  - htslib

htslib/PKGBUILD

@@ -0,0 +1,45 @@
+# Maintainer:  Andrew O'Neill <andrew at meanjollies dot com>
+# Contributor: Christopher Vittal ("viralstitch") <chris@vittal.dev>
+
+pkgname=htslib
+pkgver=1.14
+pkgrel=1
+pkgdesc='A C library for high-throughput sequencing data formats'
+arch=('x86_64')
+url="https://github.com/samtools/${pkgname}"
+license=('MIT GPL')
+depends=('bzip2' 'curl' 'xz')
+provides=('tabix')
+replaces=('tabix')
+conflicts=('tabix')
+source=("${pkgname}-${pkgver}.tar.bz2::${url}/releases/download/${pkgver}/${pkgname}-${pkgver}.tar.bz2")
+sha256sums=('ed221b8f52f4812f810eebe0cc56cd8355a5c9d21c62d142ac05ad0da147935f')
+
+build() {
+  cd "${pkgname}-${pkgver}"
+
+  ./configure \
+    --prefix=/usr \
+    --enable-libcurl \
+    --enable-plugins \
+    --with-plugin-dir=/usr/lib/htslib/plugins
+
+  make
+}
+
+check() {
+  cd "${pkgname}-${pkgver}"
+
+  make check
+}
+
+package() {
+  cd "${pkgname}-${pkgver}"
+
+  make DESTDIR=${pkgdir} install
+
+  install -Dm644 LICENSE "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
+
+  # htslib shared library comes installed as 0644
+  chmod +x ${pkgdir}/usr/lib/libhts.so.*.*
+}

htslib/lilac.py

@@ -0,0 +1,10 @@
+#!/usr/bin/env python3
+
+from lilaclib import *
+
+def pre_build():
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+
+def post_build():
+  git_add_files('PKGBUILD')
+  git_commit()

htslib/lilac.yaml

@@ -0,0 +1,8 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: starsareintherose@outlook.com
+update_on:
+  - source: github
+    github: samtools/htslib
+    use_max_tag: true