From 2eac58fc7b9ce25086973b1b31eccafd6621cb96 Mon Sep 17 00:00:00 2001
From: sukanka <su975853527@gmail.com>
Date: Sun, 10 Jul 2022 00:31:04 +0800
Subject: [PATCH] add tabixpp

---
 prepare/htslib/PKGBUILD    | 41 ++++++++++++++++++++++++++++++++++++++
 prepare/htslib/liac.yaml   | 10 ++++++++++
 prepare/htslib/lilac.py    | 14 +++++++++++++
 prepare/tabixpp/PKGBUILD   | 31 ++++++++++++++++++++++++++++
 prepare/tabixpp/lilac.py   | 14 +++++++++++++
 prepare/tabixpp/lilac.yaml |  9 +++++++++
 6 files changed, 119 insertions(+)
 create mode 100644 prepare/htslib/PKGBUILD
 create mode 100644 prepare/htslib/liac.yaml
 create mode 100644 prepare/htslib/lilac.py
 create mode 100644 prepare/tabixpp/PKGBUILD
 create mode 100644 prepare/tabixpp/lilac.py
 create mode 100644 prepare/tabixpp/lilac.yaml

diff --git a/prepare/htslib/PKGBUILD b/prepare/htslib/PKGBUILD
new file mode 100644
index 0000000000..c2861167d1
--- /dev/null
+++ b/prepare/htslib/PKGBUILD
@@ -0,0 +1,41 @@
+# Maintainer:  Andrew O'Neill <andrew at meanjollies dot com>
+# Contributor: Christopher Vittal ("viralstitch") <chris@vittal.dev>
+
+pkgname=htslib
+_pkgver=1.15.1
+pkgver=1.15.1
+pkgrel=1
+pkgdesc='A C library for high-throughput sequencing data formats'
+arch=('x86_64')
+url="https://github.com/samtools/${pkgname}"
+license=('custom')
+depends=('bzip2' 'curl' 'xz')
+provides=('tabix')
+replaces=('tabix')
+conflicts=('tabix')
+options=('staticlibs')
+source=("${pkgname}-${pkgver}.tar.bz2::${url}/releases/download/${pkgver}/${pkgname}-${pkgver}.tar.bz2")
+sha256sums=('8d7f8bf9658226942eeab70af2a22aca618577eaa8fe2ed9416ee306d5351aa1')
+
+build() {
+  cd "${pkgname}-${pkgver}"
+
+  ./configure \
+    --prefix=/usr \
+    --enable-libcurl \
+    --enable-plugins \
+    --with-plugin-dir=/usr/lib/htslib/plugins
+
+  make
+}
+
+package() {
+  cd "${pkgname}-${pkgver}"
+
+  make DESTDIR=${pkgdir} install
+
+  install -Dm644 LICENSE "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
+
+  # htslib shared library comes installed as 0644
+  chmod +x ${pkgdir}/usr/lib/libhts.so.*.*
+}
diff --git a/prepare/htslib/liac.yaml b/prepare/htslib/liac.yaml
new file mode 100644
index 0000000000..c38363d0e4
--- /dev/null
+++ b/prepare/htslib/liac.yaml
@@ -0,0 +1,10 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: sukanka
+  email: su975853527@gmail.com
+update_on:
+- source: github
+  github: samtools/htslib
+  use_max_tag: true
+- source: aur
+  aur: htslib
diff --git a/prepare/htslib/lilac.py b/prepare/htslib/lilac.py
new file mode 100644
index 0000000000..43394d7b73
--- /dev/null
+++ b/prepare/htslib/lilac.py
@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+
+def pre_build():
+    for line in edit_file('PKGBUILD'):
+        if line.startswith('_pkgver='):
+            line = f'_pkgver={_G.newver}'
+        print(line)
+    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
+
+
+def post_build():
+    git_pkgbuild_commit()
diff --git a/prepare/tabixpp/PKGBUILD b/prepare/tabixpp/PKGBUILD
new file mode 100644
index 0000000000..64c8c279a2
--- /dev/null
+++ b/prepare/tabixpp/PKGBUILD
@@ -0,0 +1,31 @@
+# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+pkgname=tabixpp
+_pkgver=1.1.1
+pkgver=1.1.1
+pkgrel=1
+pkgdesc="C++ wrapper to tabix indexer"
+arch=('x86_64')
+url="https://github.com/ekg/tabixpp"
+license=('MIT')
+depends=('htslib')
+makedepends=( 'make' 'gcc')
+optdepends=()
+source=("https://github.com/vcflib/tabixpp/archive/refs/tags/v${pkgver}.tar.gz")
+md5sums=('6441f3e3bbeb6c642edc7dea1c4cf8c3')
+
+
+build() {
+  cd "$pkgname"-${pkgver}
+  make CC=gcc HTS_HEADERS=/usr/include/htslib HTS_LIB=/usr/lib/libhts.so PREFIX=/usr
+}
+
+package() {
+  cd $srcdir/"$pkgname"-${pkgver}
+  install -Dm 755 tabix.hpp $pkgdir/usr/include/tabix.hpp
+  install -Dm 755 tabix++ $pkgdir/usr/bin/tabix++
+
+  install -Dm 755 libtabix.so.1 ${pkgdir}/usr/lib/libtabix.so.1
+  install -Dm 755 libtabix.a $pkgdir/usr/lib/libtabix.a
+
+  ln -s /usr/lib/libtabix.so.1 ${pkgdir}/usr/lib/libtabix.so
+}
diff --git a/prepare/tabixpp/lilac.py b/prepare/tabixpp/lilac.py
new file mode 100644
index 0000000000..43394d7b73
--- /dev/null
+++ b/prepare/tabixpp/lilac.py
@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+
+def pre_build():
+    for line in edit_file('PKGBUILD'):
+        if line.startswith('_pkgver='):
+            line = f'_pkgver={_G.newver}'
+        print(line)
+    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
+
+
+def post_build():
+    git_pkgbuild_commit()
diff --git a/prepare/tabixpp/lilac.yaml b/prepare/tabixpp/lilac.yaml
new file mode 100644
index 0000000000..b35727ae1e
--- /dev/null
+++ b/prepare/tabixpp/lilac.yaml
@@ -0,0 +1,9 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: sukanka
+  email: su975853527@gmail.com
+update_on:
+- source: github
+  github: vcflib/tabixpp
+  use_max_tag: true
+  prefix: 'v'