From 38697ede5aee94fbef2e00f51da31d83a130d3af Mon Sep 17 00:00:00 2001
From: Kuoi <starsareintherose@outlook.com>
Date: Fri, 2 Dec 2022 01:10:00 +0800
Subject: [PATCH] trimmomatic: build from source

---
 BioArchLinux/trimmomatic/PKGBUILD          | 33 ++++++++++++++--------
 BioArchLinux/trimmomatic/lilac.py          | 10 -------
 BioArchLinux/trimmomatic/lilac.yaml        |  6 ++++
 BioArchLinux/trimmomatic/trimmomatic       |  2 +-
 BioArchLinux/trimmomatic/trimmomatic.patch | 13 +++++++++
 5 files changed, 42 insertions(+), 22 deletions(-)
 delete mode 100644 BioArchLinux/trimmomatic/lilac.py
 create mode 100644 BioArchLinux/trimmomatic/trimmomatic.patch

diff --git a/BioArchLinux/trimmomatic/PKGBUILD b/BioArchLinux/trimmomatic/PKGBUILD
index 35f52f1b3b..f06df7a420 100644
--- a/BioArchLinux/trimmomatic/PKGBUILD
+++ b/BioArchLinux/trimmomatic/PKGBUILD
@@ -1,21 +1,32 @@
 # Maintainer: ZJLIN <zjin841126@gmail.com>
+# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
+
 pkgname=trimmomatic
+_pkgname=Trimmomatic
 pkgver=0.39
-pkgrel=5
+pkgrel=6
 pkgdesc='Trimmomatic: A flexible read trimming tool for Illumina NGS data'
 arch=('any')
 url="http://www.usadellab.org/cms/?page=trimmomatic"
 license=('GPL3')
-depends=('java-runtime>=6')
-source=("http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-$pkgver.zip"
-        "trimmomatic"
+depends=('java-runtime')
+makedepends=('java-environment=11' 'ant')
+source=("https://github.com/usadellab/Trimmomatic/archive/refs/tags/v${pkgver}.tar.gz"
+        "$pkgname"
+	"$pkgname.patch"
         )
-md5sums=('271ed9dca91132eee0c960e0ae487bcd'
-         'acd57c8656a1a398b42b50677a79df9c')
-
+md5sums=('2f80c01dd0876f7761b33ed77768a76c'
+         '0716cd4695be3e8ea6d4a5aa78f7eb85'
+         '4612f0187c29f7be68433778f884a067')
+prepare() {
+  cd $_pkgname-$pkgver
+  patch -N -i $srcdir/$pkgname.patch
+}
+build() {
+  cd $_pkgname-$pkgver
+  ant
+}
 package() {
-    mkdir -p  $pkgdir/usr/share/java/${pkgname}
-    cp -rf  $srcdir/Trimmomatic-$pkgver/* $pkgdir/usr/share/java/${pkgname}
-
-    install -Dm755 $srcdir/trimmomatic -t  $pkgdir/usr/bin
+  install -Dm 755 $srcdir/$_pkgname-$pkgver/dist/jar/$pkgname-$pkgver.jar $pkgdir/usr/share/java/$pkgname/$pkgname.jar
+  install -Dm 755 $srcdir/$pkgname -t  $pkgdir/usr/bin
 }
diff --git a/BioArchLinux/trimmomatic/lilac.py b/BioArchLinux/trimmomatic/lilac.py
deleted file mode 100644
index fcbff72939..0000000000
--- a/BioArchLinux/trimmomatic/lilac.py
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/usr/bin/env python3
-from lilaclib import *
-
-def pre_build():
-    update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
-    run_cmd(['updpkgsums'])
-
-def post_build():
-    git_add_files('PKGBUILD')
-    git_commit()
diff --git a/BioArchLinux/trimmomatic/lilac.yaml b/BioArchLinux/trimmomatic/lilac.yaml
index 98a9512437..8c7d68b730 100644
--- a/BioArchLinux/trimmomatic/lilac.yaml
+++ b/BioArchLinux/trimmomatic/lilac.yaml
@@ -2,6 +2,12 @@ build_prefix: extra-x86_64
 maintainers:
   - github: starsareintherose
     email: kuoi@bioarchlinux.org
+pre_build_script: |
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+  run_cmd(['updpkgsums'])
+post_build_script: |
+  git_add_files('PKGBUILD')
+  git_commit()
 update_on:
   - source: github
     github: usadellab/Trimmomatic 
diff --git a/BioArchLinux/trimmomatic/trimmomatic b/BioArchLinux/trimmomatic/trimmomatic
index b637261c3a..967c2a1485 100755
--- a/BioArchLinux/trimmomatic/trimmomatic
+++ b/BioArchLinux/trimmomatic/trimmomatic
@@ -1,2 +1,2 @@
 #!/usr/bin/bash
-exec /usr/bin/java -jar /usr/share/java/trimmomatic/trimmomatic-0.39.jar "$@"
+exec /usr/bin/java -jar /usr/share/java/trimmomatic/trimmomatic.jar "$@"
diff --git a/BioArchLinux/trimmomatic/trimmomatic.patch b/BioArchLinux/trimmomatic/trimmomatic.patch
new file mode 100644
index 0000000000..9095815007
--- /dev/null
+++ b/BioArchLinux/trimmomatic/trimmomatic.patch
@@ -0,0 +1,13 @@
+diff --git a/build.xml b/build.xml
+index 2efbac2..5d57a05 100644
+--- a/build.xml
++++ b/build.xml
+@@ -31,7 +31,7 @@
+ 	</target>
+ 
+ 	<target name="compile" depends="import">
+-		<javac srcdir="${src}" destdir="${dist_build}" debug="true" source="1.5" target="1.5" includeantruntime="false">
++		<javac srcdir="${src}" destdir="${dist_build}" debug="true" source="11" target="11" includeantruntime="false">
+ 			<classpath>
+ 				<fileset dir="${dist_lib}">
+ 					<include name="*.jar" />