From 85f5fb8318e507ab89b271d082358d2847ea62d9 Mon Sep 17 00:00:00 2001
From: mencian <joshua.zhuang@yahoo.com>
Date: Tue, 8 Oct 2024 16:19:40 -0500
Subject: [PATCH] Build dialign2 on OSX

---
 recipes/dialign2/build.sh                 | 14 +++++++++++++-
 recipes/dialign2/meta.yaml                | 19 +++++++++++--------
 recipes/dialign2/patches/patchdialign.txt |  4 ++--
 3 files changed, 26 insertions(+), 11 deletions(-)

diff --git a/recipes/dialign2/build.sh b/recipes/dialign2/build.sh
index cb82b1de50989..34de3c1c280e4 100644
--- a/recipes/dialign2/build.sh
+++ b/recipes/dialign2/build.sh
@@ -5,11 +5,23 @@ mkdir -p ${PREFIX}/bin
 mkdir -p ${PREFIX}/share
 mkdir -p ${PREFIX}/share/dialign2
 
+export INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
+export CFLAGS="${CFLAGS} -O3 -L${PREFIX}/lib"
+
+if [[ `uname` == "Darwin" ]]; then
+	export CFLAGS="${CFLAGS} -Wno-implicit-int -Wno-implicit-function-declaration"
+else
+	export CFLAGS="${CFLAGS}"
+fi
+
 cd src
 
 sed -i.bak "s|strcpy ( dialign_dir , \"DIALIGN2_DIR\" );|strcpy ( par_dir , \""${PREFIX}"/share/dialign2\" );|g" dialign.c
+rm -rf *.bak
 
-make CC="${CC}"
+make CC="${CC}" CFLAGS="${CFLAGS}" -j"${CPU_COUNT}"
+chmod 0755 dialign2-2
 mv dialign2-2 ${PREFIX}/bin/dialign2-2
 
 cd ../dialign2_dir
diff --git a/recipes/dialign2/meta.yaml b/recipes/dialign2/meta.yaml
index 8b04c81fa41c5..29aff0ac65dbd 100644
--- a/recipes/dialign2/meta.yaml
+++ b/recipes/dialign2/meta.yaml
@@ -6,14 +6,15 @@ package:
   version: {{ version }}
 
 source:
-  url: http://dialign.gobics.de/download/dialign_package.tgz
+  url: https://dialign.gobics.de/download/dialign_package.tgz
   sha256: {{ sha256 }}
   patches:
     - patches/patchdialign.txt
   
 build:
-  number: 7
-  skip: True  # [osx]
+  number: 8
+  run_exports:
+    - {{ pin_subpackage('dialign2', max_pin="x") }}
 
 requirements:
   build:
@@ -22,14 +23,16 @@ requirements:
 
 test:
   commands:
-    - dialign2-2 |grep usage
+    - dialign2-2 | grep "usage"
 
 about:
-  home: http://dialign.gobics.de
+  home: "https://dialign.gobics.de"
   license: LGPL
-  license_file: license/LICENSE.TXT
-  summary: DIALIGN multiple sequence alignment using various sources of external information
+  license_file: "license/LICENSE.TXT"
+  summary: "DIALIGN multiple sequence alignment using various sources of external information."
+  doc_url: "https://dialign.gobics.de"
 
 extra:
   identifiers:
-    - DOI:10.1093/nar/gkt283
+    - doi:10.1093/nar/gkt283
+    - biotools:dialign
diff --git a/recipes/dialign2/patches/patchdialign.txt b/recipes/dialign2/patches/patchdialign.txt
index d4a8242949c0f..e3a73213fbe9d 100644
--- a/recipes/dialign2/patches/patchdialign.txt
+++ b/recipes/dialign2/patches/patchdialign.txt
@@ -1,5 +1,5 @@
---- dialign_package/src/dialign.c	2005-02-21 17:32:55.000000000 +0100
-+++ dialign_package/src/dialign.c	2018-07-26 16:46:41.962909610 +0200
+--- a/src/dialign.c	2005-02-21 17:32:55.000000000 +0100
++++ b/src/dialign.c	2018-07-26 16:46:41.962909610 +0200
 @@ -294,16 +294,16 @@
  
   strcpy ( dialign_dir , "DIALIGN2_DIR" );