From 5067826682477bea7e72ce80121ea1afb9716cf5 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Wed, 4 Dec 2024 17:44:32 -0600
Subject: [PATCH] Update mustang to v3.2.4 (#52592)

* Update mustang to v3.2.4

* Update build-fail-blacklist
---
 build-fail-blacklist                |  1 -
 recipes/mustang/0001-Makefile.patch | 17 +++++++++++++++++
 recipes/mustang/build.sh            |  8 +++++---
 recipes/mustang/meta.yaml           | 25 ++++++++++++++++---------
 4 files changed, 38 insertions(+), 13 deletions(-)
 create mode 100644 recipes/mustang/0001-Makefile.patch

diff --git a/build-fail-blacklist b/build-fail-blacklist
index c679e4d7a8eee..d3452b86e22f1 100644
--- a/build-fail-blacklist
+++ b/build-fail-blacklist
@@ -612,7 +612,6 @@ recipes/genepender
 recipes/ghostx
 recipes/ls-gkm
 recipes/mosaik
-recipes/mustang
 recipes/ngmerge
 recipes/nlstradamus
 recipes/panoct
diff --git a/recipes/mustang/0001-Makefile.patch b/recipes/mustang/0001-Makefile.patch
new file mode 100644
index 0000000000000..720d7d82f37f5
--- /dev/null
+++ b/recipes/mustang/0001-Makefile.patch
@@ -0,0 +1,17 @@
+diff --git a/Makefile b/Makefile
+index f82a060..749cd4d 100644
+--- a/Makefile
++++ b/Makefile
+@@ -11,9 +11,9 @@ OBJ = $(MUSTANG)/obj
+ BIN = $(MUSTANG)/bin
+ 
+ #compiler options
+-CPP = g++ 
+-CPPFLAGS = -traditional -Wall -O3 
+-LDFLAGS =
++CPP = $(CXX)
++CPPFLAGS = -Wall -O3 -I$(PREFIX)/include -Wno-deprecated-declarations -Wno-header-guard -Wno-array-parameter
++LDFLAGS = -L$(PREFIX)/lib
+ .cpp.o:
+ 	$(CPP) $(CPPFLAGS) -c -o $@ $<
+ 
diff --git a/recipes/mustang/build.sh b/recipes/mustang/build.sh
index 138e53254d576..9fd6d5829f034 100644
--- a/recipes/mustang/build.sh
+++ b/recipes/mustang/build.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
-make
+
 mkdir -p $PREFIX/bin
-cp $SRC_DIR/bin/mustang-3.2.3 $PREFIX/bin/mustang
-chmod +x $PREFIX/bin/mustang
\ No newline at end of file
+make -j"${CPU_COUNT}"
+
+install -v -m 0755 $SRC_DIR/bin/mustang-$PKG_VERSION $PREFIX/bin
+mv $PREFIX/bin/mustang-$PKG_VERSION $PREFIX/bin/mustang
diff --git a/recipes/mustang/meta.yaml b/recipes/mustang/meta.yaml
index 3030cef73b507..f9351ac4d75fd 100644
--- a/recipes/mustang/meta.yaml
+++ b/recipes/mustang/meta.yaml
@@ -1,34 +1,41 @@
 {% set name = "mustang" %}
-{% set version = "3.2.3" %}
-
+{% set version = "3.2.4" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
-build:
-  number: 1
-
 source:
-  url: http://lcb.infotech.monash.edu.au/mustang/mustang_v3.2.3.tgz
-  md5: 8ace0194a374a60dbce15fa0b1579b44
+  url: https://lcb.infotech.monash.edu.au/mustang/mustang_v{{ version }}.tgz
+  sha256: c05e91c955f491a1fddc404a36ef963b057fd725bcc6d22ef6df1c23b26ce237
+  patches:
+    - 0001-Makefile.patch
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('mustang', max_pin="x") }}
 
 requirements:
   build:
     - make
     - {{ compiler('cxx') }}
-  run:
 
 test:
   commands:
     - mustang -h
 
 about:
-  home: http://lcb.infotech.monash.edu.au/mustang/
+  home: https://lcb.infotech.monash.edu.au/mustang
   license: file
   license_file: COPYING
   summary: "Mustang is a program that implements an algorithm for structural alignment of multiple protein structures."
+  doc_url: https://lcb.infotech.monash.edu.au/mustang
+
 extra:
   identifiers:
     - biotools:mustang
     - doi:10.1002/prot.20921
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64