2 # Makefile for building fasta3 on FreeBSD
4 # Fernan Aguero - <fernan@iib.unsam.edu.ar>
6 # we take care of doing variable assignment using the '?=' and '+='
7 # operators to preserve the value of variables if they are already
8 # defined. In FreeBSD this happens when fasta3 is build from the port or
9 # when the user has set these variables -- most notably CC and/or CFLAGS
10 # -- in /etc/make.conf
12 # Compiler executable, and optional flags
17 FASTA_HOST?= "your_fasta_host"
19 # common CFLAGS. These are the set of CFLAGS that are always used
20 COMMON_CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -c -DMAX_WORKERS=2 \
21 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT \
22 -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO \
23 -DHAS_INTTYPES -DSAMP_STATS
25 # standard options, these will be added to the common CFLAGS if
27 STANDARD_CFLAGS= -DSFCHAR="':'" -DFASTA_HOST='${FASTA_HOST}' \
28 -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC
30 # options for superfamily validations, these will be added to the common
31 # CFLAGS if selected below
32 SUPERFAMILY_CFLAGS= -DSFCHAR="'|'" -DSUPERFAMNUM -DBIG_LIB64
34 # here we define CFLAGS to be the sum of common flags plus a subset of
35 # optional flags that define our intended use.
36 # The default standard flags are selected by default, although the user
37 # can override this if s/he wants
38 CFLAGS+= ${COMMON_CFLAGS} ${STANDARD_CFLAGS}
47 # FreeBSD users BEWARE! Different threading models ahead!
49 # The threading model has changed along the way from FreeBSD-4 to
50 # FreeBSD-6. If you're building fasta3 on your own, you will need to
51 # adjust this accordingly. The default works in FreeBSD-6x (currently
52 # the recommended major version for use in production). Or better yet,
53 # use the biology/fasta3 port from the ports collection, which will use
54 # the correct threading library for your OSVERSION
60 DROPNFA_O = drop_nfa.o
63 DROPTFA_O = drop_tfa.o
65 include Makefile34m.common