From a61182f12484754f0228002b439d19584e1dd41f Mon Sep 17 00:00:00 2001
From: sukanka <su975853527@gmail.com>
Date: Fri, 15 Jul 2022 10:16:09 +0800
Subject: [PATCH] add hisat2

---
 BioArchLinux/hisat2/PKGBUILD   | 22 ++++++++++++++++++++++
 BioArchLinux/hisat2/lilac.py   | 12 ++++++++++++
 BioArchLinux/hisat2/lilac.yaml |  9 +++++++++
 3 files changed, 43 insertions(+)
 create mode 100644 BioArchLinux/hisat2/PKGBUILD
 create mode 100644 BioArchLinux/hisat2/lilac.py
 create mode 100644 BioArchLinux/hisat2/lilac.yaml

diff --git a/BioArchLinux/hisat2/PKGBUILD b/BioArchLinux/hisat2/PKGBUILD
new file mode 100644
index 0000000000..033925f411
--- /dev/null
+++ b/BioArchLinux/hisat2/PKGBUILD
@@ -0,0 +1,22 @@
+pkgname=hisat2
+pkgver=2.2.1
+pkgrel=1
+pkgdesc='A fast and sensitive alignment program for mapping next-generation sequencing reads against genomes'
+url="https://ccb.jhu.edu/software/$pkgname"
+license=(GPL3)
+arch=(x86_64)
+depends=('python' 'perl')
+source=("$pkgname-$pkgver.tar.gz::https://github.com/DaehwanKimLab/hisat2/archive/refs/tags/v2.2.1.tar.gz")
+sha256sums=('f3f4f867d0a6b1f880d64efc19deaa5788c62050e0a4d614ce98b3492f702599')
+
+build() {
+	cd "$srcdir/$pkgname-$pkgver"
+	make
+}
+
+package() {
+	cd "$srcdir/$pkgname-$pkgver"
+	for bin in hisat2 hisat2-*; do
+		install -Dm755 $bin "$pkgdir/usr/bin/$bin"
+	done
+}
diff --git a/BioArchLinux/hisat2/lilac.py b/BioArchLinux/hisat2/lilac.py
new file mode 100644
index 0000000000..f1f64315e7
--- /dev/null
+++ b/BioArchLinux/hisat2/lilac.py
@@ -0,0 +1,12 @@
+#!/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/hisat2/lilac.yaml b/BioArchLinux/hisat2/lilac.yaml
new file mode 100644
index 0000000000..bdead6f6ed
--- /dev/null
+++ b/BioArchLinux/hisat2/lilac.yaml
@@ -0,0 +1,9 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: sukanka
+  email: su975853527@gmail.com
+update_on:
+- source: github
+  github: DaehwanKimLab/hisat2
+  use_latest_release: true
+  prefix: 'v'