From 4b6fcc8380ecb24f869f1a0551661c9e4016971a Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Thu, 26 Sep 2024 23:53:21 -0500
Subject: [PATCH] trnascan-se: add aarch64/arm64 build (#50996)

---
 recipes/trnascan-se/build.sh  |  4 ++++
 recipes/trnascan-se/meta.yaml | 20 ++++++++++++++------
 2 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/recipes/trnascan-se/build.sh b/recipes/trnascan-se/build.sh
index f4f88fa388ac6..e3460852a2275 100644
--- a/recipes/trnascan-se/build.sh
+++ b/recipes/trnascan-se/build.sh
@@ -1,5 +1,6 @@
 #!/bin/bash
 
+export M4="${BUILD_PREFIX}/bin/m4"
 export INCLUDE_PATH=${PREFIX}/include
 export LIBRARY_PATH=${PREFIX}/lib
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
@@ -7,7 +8,10 @@ export CFLAGS="${CFLAGS} -O3 -I${PREFIX}/include ${LDFLAGS}"
 
 sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' tRNAscan-SE.src
 sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' src/instman.pl
+rm -rf *.bak
+rm -rf src/*.bak
 
+autoreconf -if
 ./configure CC="${CC}" CFLAGS="${CFLAGS}" --prefix="${PREFIX}"
 
 make
diff --git a/recipes/trnascan-se/meta.yaml b/recipes/trnascan-se/meta.yaml
index 5d8c1c2ed9f80..48596fa090ce3 100644
--- a/recipes/trnascan-se/meta.yaml
+++ b/recipes/trnascan-se/meta.yaml
@@ -1,16 +1,18 @@
 {% set name = "tRNAscan-SE" %}
 {% set version = "2.0.12" %}
-{% set sha256 = "96fa4af507cd918c1c623763d9260bd6ed055d091662b44314426f6bbf447251" %}
+{% set sha256 = "4b255c2c5e0255381194166f857ab2ea21c55aa7de409e201333ba615aa3dc61" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 build:
-  number: 0
+  number: 1
+  run_exports:
+    - {{ pin_subpackage('trnascan-se', max_pin="x") }}
 
 source:
-  url: http://trna.ucsc.edu/software/trnascan-se-{{ version }}.tar.gz
+  url: https://github.com/UCSC-LoweLab/tRNAscan-SE/archive/refs/tags/v{{ version }}.tar.gz
   sha256: {{ sha256 }}
   patches:
     - patches/libdir.patch
@@ -21,6 +23,7 @@ requirements:
     - make
     - autoconf
     - automake
+    - libtool
   host:
     - perl
   run:
@@ -32,13 +35,18 @@ test:
     - tRNAscan-SE -h
 
 about:
-  home: "http://lowelab.ucsc.edu/tRNAscan-SE/"
-  license: GPLv3
+  home: "https://lowelab.ucsc.edu/tRNAscan-SE/"
+  license: "GPL-3.0-or-later"
+  license_family: GPL3
   license_file: LICENSE
   summary: tRNA detection in large-scale genomic sequences
-  doc_url: "http://lowelab.ucsc.edu/tRNAscan-SE/help.html"
+  doc_url: "https://lowelab.ucsc.edu/tRNAscan-SE/help.html"
+  dev_url: "https://github.com/UCSC-LoweLab/tRNAscan-SE"
 
 extra:
   identifiers:
     - biotools:trnascan-se
     - doi:10.1093/nar/gkab688
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64