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locks; strict;
comment	@# @;


1.1
date	2022.11.06.23.01.18;	author bacon;	state Exp;
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commitid	40pk1CdjZrnHcH0E;


desc
@@


1.1
log
@biology/gffread: GFF/GTF format conversions, filtering, etc

GFF/GTF utility providing format conversions, filtering, FASTA sequence
extraction and more.  The program gffread can be used to validate,
filter, convert and perform various other operations on GFF files.
Because the program shares the same GFF parser code with Cufflinks,
Stringtie, and gffcompare, it could be used to verify that a GFF file
from a certain annotation source is correctly "understood" by these
programs.
@
text
@$NetBSD$

# Portability and package-friendliness

--- Makefile.orig	2021-07-23 14:21:36.000000000 +0000
+++ Makefile
@@@@ -1,11 +1,11 @@@@
-GCLDIR := $(if $(GCLDIR),$(GCLDIR),../gclib)
+GCLDIR := $(if $(GCLDIR),$(GCLDIR),gclib)
 
 SEARCHDIRS := -I. -I${GCLDIR}
 
 SYSTYPE :=     $(shell uname)
 
 CXX   := $(if $(CXX),$(CXX),g++)
-LINKER  := $(if $(LINKER),$(LINKER),g++)
+LINKER  := $(if $(LINKER),$(LINKER),${CXX})
 
 LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g)
 
@@@@ -15,7 +15,7 @@@@ BASEFLAGS  := -Wall -Wextra -std=c++11 $
 
 GCCV8 := $(shell expr `${CXX} -dumpversion | cut -f1 -d.` \>= 8)
 ifeq "$(GCCV8)" "1"
- BASEFLAGS += -Wno-class-memaccess
+ # BASEFLAGS += -Wno-class-memaccess
 endif
 
 CXXFLAGS := $(if $(CXXFLAGS),$(BASEFLAGS) $(CXXFLAGS),$(BASEFLAGS))
@@@@ -33,7 +33,7 @@@@ else #debug builds
     LDFLAGS += -pg
   else
     #CXXFLAGS += -g -O0 -DNDEBUG
-    CXXFLAGS += -g -O0 -DDEBUG -D_DEBUG -DGDEBUG
+    #CXXFLAGS += -g -O0 -DDEBUG -D_DEBUG -DGDEBUG
   endif
   ifneq (,$(filter %memcheck %memdebug, $(MAKECMDGOALS)))
      #use sanitizer in gcc 4.9+
@@@@ -79,10 +79,7 @@@@ OBJS := ${GCLDIR}/GBase.o ${GCLDIR}/GArg
  
 .PHONY : all
 
-all static release debug memcheck memdebug profile gprof prof: ../gclib gffread
-
-../gclib:
-	git clone https://github.com/gpertea/gclib.git ../gclib
+all static release debug memcheck memdebug profile gprof prof: ${GCLDIR} gffread
 
 $(OBJS) : $(GCLDIR)/GBase.h $(GCLDIR)/gff.h
 gffread.o : gff_utils.h $(GCLDIR)/GBase.h $(GCLDIR)/gff.h
@@@@ -97,9 +94,21 @@@@ gffread: $(OBJS) gffread.o
 
 # target for removing all object files
 
-.PHONY : clean
+.PHONY : clean install install-strip
+
 clean:
 	@@${RM} gffread gffread.o* gffread.exe $(OBJS)
 	@@${RM} core.*
 
+MKDIR	?= mkdir
+INSTALL	?= install
+STRIP	?= strip
+PREFIX	?= /usr/local
+DESTDIR	?= .
+
+install:
+	${MKDIR} -p ${DESTDIR}${PREFIX}/bin
+	${INSTALL} -c gffread ${DESTDIR}${PREFIX}/bin
 
+install-strip: install
+	${STRIP} ${DESTDIR}${PREFIX}/bin/gffread
@