From 00f6cf89875d633652e76ec451766108af583aa3 Mon Sep 17 00:00:00 2001
From: Kuoi <starsareintherose@outlook.com>
Date: Mon, 18 Apr 2022 02:17:27 +0100
Subject: [PATCH] add bbmap

---
 BioArchLinux/bbmap/PKGBUILD   | 50 +++++++++++++++++++++++++++++++++++
 BioArchLinux/bbmap/lilac.py   | 10 +++++++
 BioArchLinux/bbmap/lilac.yaml |  7 +++++
 3 files changed, 67 insertions(+)
 create mode 100644 BioArchLinux/bbmap/PKGBUILD
 create mode 100644 BioArchLinux/bbmap/lilac.py
 create mode 100644 BioArchLinux/bbmap/lilac.yaml

diff --git a/BioArchLinux/bbmap/PKGBUILD b/BioArchLinux/bbmap/PKGBUILD
new file mode 100644
index 0000000000..43cf979562
--- /dev/null
+++ b/BioArchLinux/bbmap/PKGBUILD
@@ -0,0 +1,50 @@
+# Maintainer: Clint Valentine <valentine.clint@gmail.com>
+
+pkgname=bbmap
+pkgver=37.99
+pkgrel=3
+pkgdesc="A short read aligner and other bioinformatic tools"
+arch=('x86_64')
+url=https://jgi.doe.gov/data-and-tools/bbtools/
+license=('BSD')
+depends=('jre8-openjdk>=7')
+optdepends=(
+  'env-modules: for any scripts requiring `module`' 
+  'pigz: for parallel GZIP (de)compression'
+  'samtools: for BAM output'
+)
+source=("${pkgname}"-"${pkgver}".tar.gz::https://downloads.sourceforge.net/project/"${pkgname}"/BBMap_"${pkgver}".tar.gz)
+sha256sums=('e796b399ba1a8d3ce4688b7d2d35f065754d4cdeddf09bb9a2f15ba77694f401')
+
+prepare() {
+  cd "${srcdir}"/"${pkgname}"/jni
+  make -f makefile.linux clean
+}
+
+build() {
+  cd "${srcdir}"/"${pkgname}"/jni
+  # Headers for JNI are found in this Arch Linux specific location
+  env JAVA_HOME=/usr/lib/jvm/default make -f makefile.linux
+}
+
+package() {
+  cd "${srcdir}"/"${pkgname}"
+
+  mkdir -p "${pkgdir}"/usr/share/doc/"${pkgname}"/
+  cp -r docs/* "${pkgdir}"/usr/share/doc/"${pkgname}"/
+
+  mkdir -p "${pkgdir}"/usr/share/java/"${pkgname}"/
+  cp -r config    "${pkgdir}"/usr/share/java/"${pkgname}"/
+  cp -r current   "${pkgdir}"/usr/share/java/"${pkgname}"/
+  cp -r jni       "${pkgdir}"/usr/share/java/"${pkgname}"/
+  cp -r pipelines "${pkgdir}"/usr/share/java/"${pkgname}"/
+  cp -r resources "${pkgdir}"/usr/share/java/"${pkgname}"/
+
+  for script in *.sh; do
+    sed -i s_'\bCP=.*'_CP=/usr/share/java/"${pkgname}"/current/_ "${script}"
+    sed -i s_'\bDIR=.*'_DIR=/usr/bin/_ "${script}"
+    sed -i s_'\bNATIVELIBDIR=.*'_NATIVELIBDIR=/usr/share/java/"${pkgname}"/current/jni/_ "${script}"
+
+    install -Dm775 "${script}" "${pkgdir}"/usr/bin/"${script}"
+  done
+}
diff --git a/BioArchLinux/bbmap/lilac.py b/BioArchLinux/bbmap/lilac.py
new file mode 100644
index 0000000000..fcbff72939
--- /dev/null
+++ b/BioArchLinux/bbmap/lilac.py
@@ -0,0 +1,10 @@
+#!/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/bbmap/lilac.yaml b/BioArchLinux/bbmap/lilac.yaml
new file mode 100644
index 0000000000..fdabb44968
--- /dev/null
+++ b/BioArchLinux/bbmap/lilac.yaml
@@ -0,0 +1,7 @@
+maintainers:
+  - github: starsareintherose
+    email: starsareintherose@outlook.com
+build_prefix: extra-x86_64
+update_on:
+  - source: cmd
+    cmd:  curl -sS "https://sourceforge.net/projects/bbmap/rss?path=/" | grep '<link>' | grep 'tar.gz' | head -n 1 | sed 's/_/ /g' | sed 's/.tar.gz/ /g' | awk '{print $2}'