From 581cf5e46114153bc642f013c1893726de6d1281 Mon Sep 17 00:00:00 2001
From: Kuoi <starsareintherose@outlook.com>
Date: Sun, 28 Aug 2022 15:26:35 +0100
Subject: [PATCH] nanopolish: init

---
 BioArchLinux/nanopolish/PKGBUILD   | 55 ++++++++++++++++++++++++++++++
 BioArchLinux/nanopolish/lilac.py   | 11 ++++++
 BioArchLinux/nanopolish/lilac.yaml | 14 ++++++++
 3 files changed, 80 insertions(+)
 create mode 100644 BioArchLinux/nanopolish/PKGBUILD
 create mode 100644 BioArchLinux/nanopolish/lilac.py
 create mode 100644 BioArchLinux/nanopolish/lilac.yaml

diff --git a/BioArchLinux/nanopolish/PKGBUILD b/BioArchLinux/nanopolish/PKGBUILD
new file mode 100644
index 0000000000..d89ce35892
--- /dev/null
+++ b/BioArchLinux/nanopolish/PKGBUILD
@@ -0,0 +1,55 @@
+# Maintainer: Chocobo1 <chocobo1 AT archlinux DOT net>
+
+pkgname=nanopolish
+pkgver=0.14.0
+pkgrel=1
+pkgdesc="Provide signal-level analysis of Oxford Nanopore sequencing data"
+arch=('x86_64')
+url="https://github.com/jts/nanopolish"
+license=('MIT')
+depends=('glibc' 'hdf5' 'htslib' 'zlib')
+makedepends=('git' 'eigen' 'wget')
+source=("git+https://github.com/jts/nanopolish.git#tag=v$pkgver")
+sha256sums=('SKIP'
+            '8863f56ef51672a4c6c50aeaea2e0e1b866a06bf4d4ca14006680f698e795a26')
+
+prepare() {
+  cd "nanopolish"
+
+  git submodule update --init --recursive --remote
+
+#  patch -Np1 -i "$srcdir/0001-Fix-include-path-for-system-installed-eigen-library.patch"
+#  patch -Np1 -i "$srcdir/0002-Allow-users-to-supply-htslib-include-path-from-comma.patch"
+}
+
+build() {
+  cd "nanopolish"
+
+  make \
+    EIGEN=noinstall \
+    HDF5=noinstall \
+    HTS=noinstall \
+    EIGEN_INCLUDE="-I/usr/include/eigen3" \
+    H5_INCLUDE="-I/usr/include" \
+    HTS_INCLUDE="-I/usr/include/htslib"
+}
+
+check() {
+  cd "nanopolish"
+
+  make \
+    EIGEN=noinstall \
+    HDF5=noinstall \
+    HTS=noinstall \
+    EIGEN_INCLUDE="-I/usr/include/eigen3" \
+    H5_INCLUDE="-I/usr/include" \
+    HTS_INCLUDE="-I/usr/include/htslib" \
+    test
+}
+
+package() {
+  cd "nanopolish"
+
+  install -Dm755 "nanopolish" -t "$pkgdir/usr/bin"
+  install -Dm644 "LICENSE" -t "$pkgdir/usr/share/licenses/nanopolish"
+}
diff --git a/BioArchLinux/nanopolish/lilac.py b/BioArchLinux/nanopolish/lilac.py
new file mode 100644
index 0000000000..8a6e65aeba
--- /dev/null
+++ b/BioArchLinux/nanopolish/lilac.py
@@ -0,0 +1,11 @@
+#!/usr/bin/env python3
+
+from lilaclib import *
+
+def pre_build():
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+  run_cmd(['updpkgsums'])
+
+def post_build():
+  git_add_files('PKGBUILD')
+  git_commit()
diff --git a/BioArchLinux/nanopolish/lilac.yaml b/BioArchLinux/nanopolish/lilac.yaml
new file mode 100644
index 0000000000..bc4d292ca6
--- /dev/null
+++ b/BioArchLinux/nanopolish/lilac.yaml
@@ -0,0 +1,14 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: kuoi@bioarchlinux.org
+update_on:
+  - source: github
+    github: jts/nanopolish
+    use_max_tag: true
+    prefix: 'v'
+  - alias: alpm-lilac
+    alpm: htslib
+    strip_release: true
+repo_depends:
+  - htslib