From 6e92cb85dc3c8865675740e45864d598e2ba2c54 Mon Sep 17 00:00:00 2001
From: starsareintherose <starsareintherose@outlook.com>
Date: Mon, 23 Aug 2021 02:44:31 +0800
Subject: [PATCH] add beast2

---
 beast2/PKGBUILD              | 31 +++++++++++++++++++++++++++++++
 beast2/beauti.desktop        | 16 ++++++++++++++++
 beast2/densitree.desktop     | 18 ++++++++++++++++++
 beast2/lilac.py              | 10 ++++++++++
 beast2/lilac.yaml            |  8 ++++++++
 beast2/logcombiner.desktop   | 16 ++++++++++++++++
 beast2/treeannotator.desktop | 17 +++++++++++++++++
 7 files changed, 116 insertions(+)
 create mode 100644 beast2/PKGBUILD
 create mode 100755 beast2/beauti.desktop
 create mode 100755 beast2/densitree.desktop
 create mode 100644 beast2/lilac.py
 create mode 100644 beast2/lilac.yaml
 create mode 100755 beast2/logcombiner.desktop
 create mode 100755 beast2/treeannotator.desktop

diff --git a/beast2/PKGBUILD b/beast2/PKGBUILD
new file mode 100644
index 0000000000..5bc2f07711
--- /dev/null
+++ b/beast2/PKGBUILD
@@ -0,0 +1,31 @@
+# Maintainer: Malacology <guoyizhang at malacology dot com>
+# Contributor: Malacology <guoyizhang at malacology dot com>
+
+pkgname=beast2
+pkgver=2.6.4
+pkgrel=1
+pkgdesc="Bayesian Evolutionary Analysis by Sampling Trees"
+arch=('x86_64')
+url="http://www.beast2.org/"
+license=('LGPL-2.1 License')
+provides=("beast2")
+source=("https://github.com/CompEvol/beast2/releases/download/v${pkgver}/BEAST.v${pkgver}.Linux.tgz" "beauti.desktop" "densitree.desktop" "logcombiner.desktop" "treeannotator.desktop")
+sha256sums=('4f80e2920eb9d87f3e9f64433119774dc67aca390fbd13dd480f852e3f8701a4'
+            '83fba4c776fd29d6852c9c412c31d98bff657e2d2d2763dfe46d4c6174a9495f'
+            '40d86086691b6cb91d0af54e5dc53d6693e084242ff3cc77862650ca78667c3d'
+            'c2057c6ac656e13dcfbdf580a696bc79cb22c3d5270d546eac3e2fb42d620f20'
+            '960a2d9030105156e178fe8fd5a8329cf10af1e16141623da47f649f059906b0')
+depends=(
+	'java-runtime'
+)
+package() {
+    install -dm755 "$pkgdir"/usr/{bin,share/{beast2,applications}}
+    mv "$srcdir"/beast/* "$pkgdir"/usr/share/beast2
+        
+    ln -s /usr/share/beast2/bin/beauti ${pkgdir}/usr/bin/beauti
+    ln -s /usr/share/beast2/bin/logcombiner ${pkgdir}/usr/bin/logcombiner
+    ln -s /usr/share/beast2/bin/treeannotator ${pkgdir}/usr/bin/treeannotator
+    ln -s /usr/share/beast2/bin/densitree ${pkgdir}/usr/bin/densitree
+    
+    install -m 755 ${srcdir}/*.desktop ${pkgdir}/usr/share/applications
+}
diff --git a/beast2/beauti.desktop b/beast2/beauti.desktop
new file mode 100755
index 0000000000..714a5b21c8
--- /dev/null
+++ b/beast2/beauti.desktop
@@ -0,0 +1,16 @@
+[Desktop Entry]
+Categories=
+Encoding=UTF-8
+Exec=/usr/share/beast2/bin/beauti
+Icon=/usr/share/beast2/images/beauti.png
+MimeType=
+Name=beauti
+ServiceTypes=
+SwallowExec=
+SwallowTitle=
+Terminal=false
+TerminalOptions=
+Type=Application
+X-KDE-SubstituteUID=false
+X-KDE-Username=root
+X-GNOME-UsesNotifications=true
diff --git a/beast2/densitree.desktop b/beast2/densitree.desktop
new file mode 100755
index 0000000000..88cdc3b8e0
--- /dev/null
+++ b/beast2/densitree.desktop
@@ -0,0 +1,18 @@
+[Desktop Entry]
+Categories=
+Encoding=UTF-8
+Exec=/usr/share/beast2/bin/densitree
+GenericName=
+GenericName[zh]=
+Icon=/usr/share/beast2/images/DensiTree.png
+MimeType=
+Name=densitree
+Name[zh]=densitree
+ServiceTypes=
+SwallowExec=
+SwallowTitle=
+Terminal=false
+TerminalOptions=
+Type=Application
+X-KDE-SubstituteUID=false
+X-KDE-Username=root
diff --git a/beast2/lilac.py b/beast2/lilac.py
new file mode 100644
index 0000000000..8c66f58ed6
--- /dev/null
+++ b/beast2/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()
diff --git a/beast2/lilac.yaml b/beast2/lilac.yaml
new file mode 100644
index 0000000000..a669cd4b64
--- /dev/null
+++ b/beast2/lilac.yaml
@@ -0,0 +1,8 @@
+build_prefix: multilib
+maintainers:
+  - github: starsareintherose
+    email: starsareintherose@outlook.com
+update_on:
+  - source: github
+    github: CompEvol/beast2
+    use_latest_release: true
diff --git a/beast2/logcombiner.desktop b/beast2/logcombiner.desktop
new file mode 100755
index 0000000000..06bcc6f758
--- /dev/null
+++ b/beast2/logcombiner.desktop
@@ -0,0 +1,16 @@
+[Desktop Entry]
+Categories=
+Encoding=UTF-8
+Exec=/usr/share/beast2/bin/logcombiner
+Icon=/usr/share/beast2/images/beast.png
+MimeType=
+Name=logcombiner
+Name[zh]=logcombiner
+ServiceTypes=
+SwallowExec=
+SwallowTitle=
+Terminal=false
+TerminalOptions=
+Type=Application
+X-KDE-SubstituteUID=false
+X-KDE-Username=root
diff --git a/beast2/treeannotator.desktop b/beast2/treeannotator.desktop
new file mode 100755
index 0000000000..963a448e10
--- /dev/null
+++ b/beast2/treeannotator.desktop
@@ -0,0 +1,17 @@
+[Desktop Entry]
+Categories=
+Encoding=UTF-8
+Exec=/usr/share/beast2/bin/treeannotator
+GenericName=
+GenericName[zh]=
+Icon=/usr/share/beast2/images/beast.png
+MimeType=
+Name=treeannotator
+ServiceTypes=
+SwallowExec=
+SwallowTitle=
+Terminal=false
+TerminalOptions=
+Type=Application
+X-KDE-SubstituteUID=false
+X-KDE-Username=root