gatk: build from source

BioArchLinux/gatk/PKGBUILD

@@ -1,22 +1,32 @@
-# Maintainer: Clint Valentine <valentine.clint@gmail.com>
-# Contributer: Christian Krause ("wookietreiber") <christian.krause@mailbox.org>
-
 pkgname=gatk
 pkgver=4.4.0.0
 pkgrel=1
-pkgdesc="Variant discovery in high-throughput bioinformatics sequencing data"
+pkgdesc="Genome Analysis Toolkit https://doi.org/10.1101/gr.107524.110"
 arch=('any')
 url=https://software.broadinstitute.org/"${pkgname}"
 license=('BSD')
+makedepends=('git' 'java-environment=17' 'git-lfs')
+depends=('java-runtime=17' 'python' 'r')
+source=("gatk.sh")
+sha256sums=('acc059e37c9e9e9053815095d3eecd00cd115d22f4c14bc4b97d7a5be13234c4')
 
-depends=('java-runtime>=8' 'python' 'r')
-source=("https://github.com/broadinstitute/gatk/releases/download/${pkgver}/gatk-${pkgver}.zip")
-sha256sums=('444600f7b38b46ad0b3606b7d40ce921e0ff1910a50165872f1c73c7c4a1a390')
 
+prepare() {
+  cd "${srcdir}"
+  git clone https://github.com/broadinstitute/gatk.git "${pkgname}"
+  cd $pkgname
+  git checkout "${pkgver}"
+  git lfs install
+}
+
+build() {
+  cd "${srcdir}"/"${pkgname}"
+  ./gradlew localJar
+}
 
 package() {
-  cd "${srcdir}"/"${pkgname}"-"${pkgver}"
+  install -Dm755 gatk.sh "${pkgdir}"/usr/bin/gatk
-  install -Dm755 gatk $pkgdir/usr/bin/$pkgname
+  cd "${srcdir}"/"${pkgname}"
-  install -Dm644 "gatk-package-${pkgver}-local.jar" "${pkgdir}/usr/share/java/${pkgname}/GenomeAnalysisTK.jar"
+  install -Dm644 build/libs/gatk-package-"${pkgver}"-SNAPSHOT-local.jar "${pkgdir}"/usr/share/java/"${pkgname}"/GenomeAnalysisTK.jar
-  install -Dm644 "gatk-completion.sh" "${pkgdir}/usr/share/bash-completion/completions/gatk"
 }
+

BioArchLinux/gatk/gatk.sh

@@ -0,0 +1,38 @@
+#!/bin/bash
+set -eou pipefail
+
+default_jvm_mem_opts="-Xms512m -Xmx1g"
+jvm_mem_opts=""
+jvm_prop_opts=""
+pass_args=""
+
+for arg in "$@"; do
+  case $arg in
+    '-D'*)
+      jvm_prop_opts="$jvm_prop_opts $arg"
+      ;;
+    '-XX'*)
+      jvm_prop_opts="$jvm_prop_opts $arg"
+      ;;
+     '-Xm'*)
+      jvm_mem_opts="$jvm_mem_opts $arg"
+      ;;
+     *)
+      pass_args="$pass_args $arg"
+      ;;
+  esac
+done
+
+if [ "$jvm_mem_opts" == "" ]; then
+  jvm_mem_opts="$default_jvm_mem_opts"
+fi
+
+pass_arr=($pass_args)
+if [[ ${pass_arr[0]:=} == org* ]]
+then
+  eval java $jvm_mem_opts $jvm_prop_opts -cp '/usr/share/java/gatk/GenomeAnalysisTK.jar' $pass_args
+else
+  eval java $jvm_mem_opts $jvm_prop_opts -jar '/usr/share/java/gatk/GenomeAnalysisTK.jar' $pass_args
+fi
+exit
+

BioArchLinux/gatk/lilac.py

@@ -1,11 +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()
-    update_aur_repo()

BioArchLinux/gatk/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_pkgbuild_commit()
+  update_aur_repo()
 update_on:
   - source: github
     github: broadinstitute/gatk