From 25ef0a10b161669c6a1fe6bd46f652c517111206 Mon Sep 17 00:00:00 2001
From: mencian <joshua.zhuang@yahoo.com>
Date: Thu, 24 Oct 2024 16:03:13 -0500
Subject: [PATCH] clean up recipe

---
 recipes/augustus/build.sh                    |  3 +++
 recipes/augustus/patches/0001-Makefile.patch |  5 +++--
 recipes/augustus/patches/utrrnaseq.patch     | 19 +++++++++++++++----
 3 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/recipes/augustus/build.sh b/recipes/augustus/build.sh
index d82859321137b..369ec2192cfa7 100644
--- a/recipes/augustus/build.sh
+++ b/recipes/augustus/build.sh
@@ -7,6 +7,7 @@ export LIBPATH="-L${PREFIX}/lib"
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 -DUSE_BOOST -I${PREFIX}/include"
 
+mkdir -p ${PREFIX}/bin
 mkdir -p ${PREFIX}/scripts
 mkdir -p ${PREFIX}/config
 
@@ -53,6 +54,8 @@ cd ..
 
 ## End build perl
 
+chmod 0755 bin/augustus
+mv bin/* $PREFIX/bin/
 mv scripts/* $PREFIX/bin/
 mv config/* $PREFIX/config/
 
diff --git a/recipes/augustus/patches/0001-Makefile.patch b/recipes/augustus/patches/0001-Makefile.patch
index c1d8970167b1e..29177a5f9654f 100644
--- a/recipes/augustus/patches/0001-Makefile.patch
+++ b/recipes/augustus/patches/0001-Makefile.patch
@@ -1,5 +1,5 @@
 diff --git a/Makefile b/Makefile
-index a26b40c..b061356 100644
+index a26b40c..b2ccb6a 100644
 --- a/Makefile
 +++ b/Makefile
 @@ -26,20 +26,26 @@ clean:
@@ -7,10 +7,11 @@ index a26b40c..b061356 100644
  	fi
  
 -PREFIX = /usr/local
+-INSTALLDIR = /opt/augustus-$(AUGVERSION)
 +# DESTDIR is usually the empty string but can be set for staging
 +prefix ?= $(PREFIX)
 +bindir = $(DESTDIR)$(prefix)/bin
- INSTALLDIR = /opt/augustus-$(AUGVERSION)
++INSTALLDIR = $(prefix)/share/augustus-$(AUGVERSION)
  
  install:
 -	if [ ! $(PWD) -ef $(INSTALLDIR) ] ; then \
diff --git a/recipes/augustus/patches/utrrnaseq.patch b/recipes/augustus/patches/utrrnaseq.patch
index 33ed805d73488..4befbfaf97c85 100644
--- a/recipes/augustus/patches/utrrnaseq.patch
+++ b/recipes/augustus/patches/utrrnaseq.patch
@@ -1,6 +1,17 @@
---- a/auxprogs/utrrnaseq/Makefile	2022-09-23 10:06:14.000000000 -0700
-+++ b/auxprogs/utrrnaseq/Makefile	2022-10-08 10:15:31.359607884 -0700
-@@ -29,6 +29,7 @@
+diff --git a/auxprogs/utrrnaseq/Makefile b/auxprogs/utrrnaseq/Makefile
+index 134c5c5..63fa103 100644
+--- a/auxprogs/utrrnaseq/Makefile
++++ b/auxprogs/utrrnaseq/Makefile
+@@ -3,7 +3,7 @@
+ include ../../common.mk
+ 
+ CXX ?= g++
+-CXXFLAGS := -Wall -O0 -pedantic -fmessage-length=0 ${CXXFLAGS}
++CXXFLAGS := -Wall -O3 -pedantic -fmessage-length=0 -std=c++14 ${CXXFLAGS}
+ INCLS   += $(INCLUDE_PATH_BOOST) # set boost include path in INCLUDE_PATH_BOOST, if boost is not installed system-wide
+ LDFLAGS += $(LIBRARY_PATH_BOOST) # set boost library path in LIBRARY_PATH_BOOST, if boost is not installed system-wide
+ 
+@@ -29,6 +29,7 @@ utrrnaseq: $(OBJS)
  	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS)
  	@echo 'Finished building target: $@'
  	@echo ' '
@@ -8,7 +19,7 @@
  
  $(OBJS): $(OBJ_DIR)/%.o: $(SRC_DIR)/%.cpp
  	@echo 'Building file: $<'
-@@ -55,5 +56,6 @@
+@@ -55,5 +56,6 @@ clean_test:
  clean: clean_test
  	rm -rf $(OBJS) $(DEPS) $(OBJ_DIR) utrrnaseq
  	@echo ' '