From 550b572d3fb2a421dc2b03fdfb7eaca3c7cb808b Mon Sep 17 00:00:00 2001
From: Kuoi <kuoi@bioarchlinux.org>
Date: Fri, 16 Feb 2024 03:14:44 +0800
Subject: [PATCH] trinityrnaseq: init

---
 BioArchLinux/trinityrnaseq/PKGBUILD     | 103 ++++++++++++++++++++++++
 BioArchLinux/trinityrnaseq/lilac.yaml   |  14 ++++
 BioArchLinux/trinityrnaseq/string.patch |  12 +++
 3 files changed, 129 insertions(+)
 create mode 100644 BioArchLinux/trinityrnaseq/PKGBUILD
 create mode 100644 BioArchLinux/trinityrnaseq/lilac.yaml
 create mode 100644 BioArchLinux/trinityrnaseq/string.patch

diff --git a/BioArchLinux/trinityrnaseq/PKGBUILD b/BioArchLinux/trinityrnaseq/PKGBUILD
new file mode 100644
index 0000000000..07e560f247
--- /dev/null
+++ b/BioArchLinux/trinityrnaseq/PKGBUILD
@@ -0,0 +1,103 @@
+# Maintainer: Malacology <guoyizhang at malacology dot net>
+# Contributor: Malacology <guoyizhang at malacology dot net>
+basename=trinityrnaseq
+pkgname=('trinityrnaseq' 'trinityrnaseq-doc' 'trinityrnaseq-extra')
+_pkgname=Trinity
+pkgver=2.15.1
+pkgrel=0
+pkgdesc="Transcriptome assembler for RNA-seq reads \
+	 https://doi.org/10.1038%2Fnbt.1883"
+url="https://github.com/Trinotate/Trinotate/wiki"
+license=('BSD-3-Clause')
+makedepends=('git' 'cmake' 'make' 'python' 'rsync')
+source=("git+https://github.com/trinityrnaseq/trinityrnaseq.git#tag=$_pkgname-v$pkgver"
+	"string.patch")
+sha256sums=('SKIP'
+            '9304eae411d76a6ce1846ed06e7311b35175638a74ec6277909ef9d4ba71769b')
+
+prepare(){
+  cd $srcdir/$pkgname
+  git submodule update --init --recursive
+  patch -p1 < $srcdir/string.patch
+}
+
+build() {
+  cd $srcdir/$pkgname
+  make 
+  make plugins
+}
+
+package_trinityrnaseq() {
+  depends=('perl' 'bash' 'glibc' 'java-runtime' 'python' 'zlib')
+  # 'xz' 'bzip2' 'curl'
+  arch=('x86_64')
+
+  cd $srcdir/$basename
+  mkdir -p $pkgdir/usr/{share/{$pkgname,java},bin}
+
+  ls 
+
+  # Dir 
+for dir in Analysis PerlLib PyLib
+do
+  find $dir -type f -exec install -D -m 755 {} $pkgdir/usr/share/$basename/$dir \;
+done
+
+  # Bin
+for binadir in Chrysalis/bin Inchworm/bin 
+do
+  find $binadir -type f -exec install -D -m 755 {} $pkgdir/usr/bin/ \;
+done
+
+  install -Dm755 Trinity $pkgdir/usr/bin/Trinity
+  install -Dm755 trinity-plugins/BIN/seqtk-trinity $pkgdir/usr/bin/seqtk-trinity
+  
+  # Java
+  install -Dm755 Butterfly/Butterfly.jar $pkgdir/usr/share/Butterfly.jar
+
+  # Plugin
+  # Todo: check trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs
+  plugins=(
+    "trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl"
+    "trinity-plugins/COLLECTL/util/collectl_dat_to_time_matrix.py"
+    "trinity-plugins/COLLECTL/util/plot_time_vs_resource.Rscript"
+    "trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py"
+    "trinity-plugins/bamsifter/bamsifter"
+    "trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py"
+  )
+  for plugin in "${plugins[@]}"
+  do
+    ls $srcdir/$basename/$plugin 
+    install -Dm755 $srcdir/$basename/$plugin $pkgdir/usr/share/$pkgname/$plugin
+  done
+
+  # Util
+  find util -type f -exec install -D -m 755 {} $pkgdir/usr/share/$basename/util \;
+}
+
+package_trinityrnaseq-doc(){
+  arch=('any')
+  cd $srcdir/$basename
+  mkdir -p $pkgdir/usr/share/doc/$basename/wiki
+
+for note in developer.notes Changelog.txt README README.md
+do
+  install -Dm644 $note $pkgdir/usr/share/doc/$basename/$note
+done
+
+  find trinityrnaseq.wiki -type f -exec install -D -m 644 {} $pkgdir/usr/share/doc/$basename/wiki \;
+
+}
+
+package_trinityrnaseq-extra(){
+  depends=('bash' 'perl')
+  arch=('x86_64')
+
+  cd $srcdir/$basename
+  mkdir -p $pkgdir/usr/share/$basename/{trinity_ext_sample_data,sample_data}
+
+for datadir in trinity_ext_sample_data sample_data 
+do
+  find $datadir -type f -exec install -D -m 755 {} $pkgdir/usr/share/$basename/$datadir/ \;
+done
+}
diff --git a/BioArchLinux/trinityrnaseq/lilac.yaml b/BioArchLinux/trinityrnaseq/lilac.yaml
new file mode 100644
index 0000000000..7324cea522
--- /dev/null
+++ b/BioArchLinux/trinityrnaseq/lilac.yaml
@@ -0,0 +1,14 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: kuoi@bioarchlinux.org
+pre_build_script: |
+  update_pkgver_and_pkgrel(_G.newver)
+post_build_script: |
+  git_pkgbuild_commit()
+  update_aur_repo()
+update_on:
+  - source: github
+    github: trinityrnaseq/trinityrnaseq
+    use_max_tag: true
+    include_regex: Trinity-v(\d+.\d+.\d+)
diff --git a/BioArchLinux/trinityrnaseq/string.patch b/BioArchLinux/trinityrnaseq/string.patch
new file mode 100644
index 0000000000..8647aad3ac
--- /dev/null
+++ b/BioArchLinux/trinityrnaseq/string.patch
@@ -0,0 +1,12 @@
+diff --git a/trinity-plugins/bamsifter/sift_bam_max_cov.cpp b/trinity-plugins/bamsifter/sift_bam_max_cov.cpp
+index e8ecbcf..ccdbd27 100644
+--- a/trinity-plugins/bamsifter/sift_bam_max_cov.cpp
++++ b/trinity-plugins/bamsifter/sift_bam_max_cov.cpp
+@@ -10,6 +10,7 @@
+ #include <set>
+ #include <utility>
+ #include <vector>
++#include <string>
+ 
+ #include "htslib/sam.h"
+ #include "htslib/bgzf.h"