add samtools

samtools/PKGBUILD

@@ -0,0 +1,56 @@
+# Maintainer: r6eve <r6eve at acm dot org>
+# Former Maintainer (thnaks!): Christopher Vittal ("viralstitch") <chris@vittal.dev>
+# Former Maintainer (thans!) : Alex Peltzer ("alexpe87") <alexpe.aur@mailbox.org>
+# Former Maintainer (thanks dude!) : Christian Krause ("wookietreiber") <christian.krause@mailbox.org>
+# Contributor: Markus Heuser <markus.heuser@web.de>
+
+pkgname=samtools
+pkgver=1.14
+pkgrel=1
+pkgdesc="tools for manipulating next-generation sequencing data"
+arch=('i686' 'x86_64')
+url="http://www.htslib.org/"
+license=('custom')
+depends=('htslib>=1.14')
+optdepends=('luajit: needed for r2plot.lua vcfutils.lua')
+source=("${pkgname}-${pkgver}.tar.bz2"::"https://github.com/samtools/samtools/releases/download/${pkgver}/${pkgname}-${pkgver}.tar.bz2")
+sha256sums=('9341dabaa98b0ea7d60fd47e42af25df43a7d3d64d8e654cdf852974546b7d74')
+
+prepare() {
+  cd "${srcdir}/${pkgname}-${pkgver}"
+
+  # prevent shipped htslib to be used
+  rm -rf "htslib-${pkgver}" || exit 1
+}
+
+build() {
+  cd "${srcdir}/${pkgname}-${pkgver}"
+
+  ./configure \
+    --prefix=/usr \
+    --with-htslib=system
+
+  make
+}
+
+check() {
+  cd "${srcdir}/${pkgname}-${pkgver}"
+
+  make check
+}
+
+package() {
+  cd ${srcdir}/${pkgname}-${pkgver}
+
+  make DESTDIR=${pkgdir} install
+
+  # Install non-Perl misc/ programs
+  for file in misc/*.lua; do
+    install -Dm755 "${file}" "${pkgdir}/usr/bin/$(basename "${file}")"
+  done
+
+  install -d "${pkgdir}/usr/include/bam"
+  install -Dm644 *.h "${pkgdir}/usr/include/bam"
+
+  install -Dm644 LICENSE "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
+}

samtools/lilac.py

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+#!/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()

samtools/lilac.yaml

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