post-extract:

	@ cp ${FILESDIR}/Makefile.freebsd ${WRKSRC}

#

# Makefile for building fasta3 on FreeBSD

#

# Fernan Aguero - <fernan@iib.unsam.edu.ar>

# we take care of doing variable assignment using the '?=' and '+='

# operators to preserve the value of variables if they are already

# defined. In FreeBSD this happens when fasta3 is build from the port or

# when the user has set these variables -- most notably CC and/or CFLAGS

# -- in /etc/make.conf

# Compiler executable, and optional flags

CC?=		gcc

CFLAGS?=	-g -O2

# your FASTA host

FASTA_HOST?=	"your_fasta_host"

# common CFLAGS. These are the set of CFLAGS that are always used

COMMON_CFLAGS=	-DSHOWSIM -DUNIX -DTIMES -DHZ=100 -c -DMAX_WORKERS=2 \

		-DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT \

		-D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO \

		-DHAS_INTTYPES -DSAMP_STATS

# standard options, these will be added to the common CFLAGS if

# selected below

STANDARD_CFLAGS=	-DSFCHAR="':'" -DFASTA_HOST='${FASTA_HOST}' \

			-D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC

# options for superfamily validations, these will be added to the common

# CFLAGS if selected below

SUPERFAMILY_CFLAGS=	-DSFCHAR="'|'" -DSUPERFAMNUM -DBIG_LIB64

# here we define CFLAGS to be the sum of common flags plus a subset of

# optional flags that define our intended use.

# The default standard flags are selected by default, although the user

# can override this if s/he wants

CFLAGS+=	${COMMON_CFLAGS} ${STANDARD_CFLAGS}

XDIR?=		/usr/local/bin

LIB_M+=		-lm

HFLAGS+=	-o

NFLAGS+=	-o

# FreeBSD users BEWARE! Different threading models ahead!

# The threading model has changed along the way from FreeBSD-4 to

# FreeBSD-6. If you're building fasta3 on your own, you will need to

# adjust this accordingly. The default works in FreeBSD-6x (currently

# the recommended major version for use in production). Or better yet,

# use the biology/fasta3 port from the ports collection, which will use

# the correct threading library for your OSVERSION

THR_SUBS?=	pthr_subs2

THR_LIBS?=	-lpthread

THR_CC?=	

DROPNFA_O = drop_nfa.o

DROPGSW_O = dropgsw.o

DROPRSS_O = dropnsw.o

DROPTFA_O = drop_tfa.o

include Makefile34m.common