From 1cc92b8ad22f6f0a91cea8947236652cef39ceed Mon Sep 17 00:00:00 2001
From: mencian <joshua.zhuang@yahoo.com>
Date: Thu, 26 Sep 2024 15:12:48 -0500
Subject: [PATCH 1/2] trnascan-se: add aarch64/arm64 build

---
 recipes/trnascan-se/build.sh  |  3 +++
 recipes/trnascan-se/meta.yaml | 16 ++++++++++++----
 2 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/recipes/trnascan-se/build.sh b/recipes/trnascan-se/build.sh
index f4f88fa388ac6..7a8e9f1e277ab 100644
--- a/recipes/trnascan-se/build.sh
+++ b/recipes/trnascan-se/build.sh
@@ -7,7 +7,10 @@ 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..fd0305e59cc06 100644
--- a/recipes/trnascan-se/meta.yaml
+++ b/recipes/trnascan-se/meta.yaml
@@ -7,7 +7,9 @@ package:
   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
@@ -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

From 2ca3cb6f452292c0f4dfe7277f38627f1cab19c3 Mon Sep 17 00:00:00 2001
From: mencian <joshua.zhuang@yahoo.com>
Date: Thu, 26 Sep 2024 15:38:31 -0500
Subject: [PATCH 2/2] change source URL

---
 recipes/trnascan-se/build.sh  | 1 +
 recipes/trnascan-se/meta.yaml | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/recipes/trnascan-se/build.sh b/recipes/trnascan-se/build.sh
index 7a8e9f1e277ab..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"
diff --git a/recipes/trnascan-se/meta.yaml b/recipes/trnascan-se/meta.yaml
index fd0305e59cc06..48596fa090ce3 100644
--- a/recipes/trnascan-se/meta.yaml
+++ b/recipes/trnascan-se/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "tRNAscan-SE" %}
 {% set version = "2.0.12" %}
-{% set sha256 = "96fa4af507cd918c1c623763d9260bd6ed055d091662b44314426f6bbf447251" %}
+{% set sha256 = "4b255c2c5e0255381194166f857ab2ea21c55aa7de409e201333ba615aa3dc61" %}
 
 package:
   name: {{ name|lower }}
@@ -12,7 +12,7 @@ build:
     - {{ 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