1 # makefile for fasta3, fasta3_t. Use makefile.pvm for pvcompxx.
2 # this file works for DEC Alphas
4 # this file supports mmap()'ed databases in BLAST2 format use -DUSE_MMAP
5 # for mmap()ed BLAST2 format.
7 # the -DDEBUG option provides additional debugging information, particularly
8 # with -D on the command line.
10 # use -DBIG_LIB64 to generate 64-bit offsets in map_db .xin files
12 # changed to gcc-3.3 for MacOSX Tiger because of problems with Altivec
15 # in my hands, gcc-4.0 is about 40% slower than gcc-3.3 on the Altivec code
16 #CC= gcc-4.0 -g -falign-loops=32 -O3 -mcpu=7450 -maltivec -mpim-altivec -DSW_ALTIVEC
18 CC= gcc-3.3 -g -falign-loops=32 -O3 -mcpu=7450 -faltivec -DSW_ALTIVEC
19 #CC= gcc-3.3 -g -DDEBUG -mcpu=7450 -faltivec -DSW_ALTIVEC
20 #CC= cc -g -Wall -pedantic -faltivec -DSW_ALTIVEC
22 # standard line for normal searching
23 CFLAGS= -DSHOWSIM -DM10_CONS -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=4 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"xs00.achs.virginia.edu/fasta_www/cgi"' -DUSE_MMAP -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DPGM_DOC
25 #CFLAGS= -DSHOWSIM -DM10_CONS -DUNIX -DTIMES -DHZ=60 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"xs00.achs.virginia.edu/fasta_www/cgi"' -DUSE_MMAP -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DPGM_DOC -DSUPERFAMNUM -DSFCHAR="'|'"
27 # add for MySQL support
28 # -I/usr/local/mysql/include -DMYSQL_DB
39 #THR_SUBS = uthr_subs2
43 # for SGI with current pthreads
44 #THR_SUBS = pthr_subs2
45 #THR_LIBS = -lpthreads
48 # for IBM with current pthreads
50 #THR_SUBS = ibm_pthr_subs2
51 #THR_LIBS = -lpthreads
56 #XDIR = /home/slib/bin/MACOSX/
57 #XDIR = /Users/seqprg/bin
61 DROPNFA_O = drop_nfa.o
62 DROPTFA_O = drop_tfa.o
63 DROPGSW_O = dropgsw.o smith_waterman_altivec.o
64 DROPRSS_O = dropgsw.o smith_waterman_altivec.o
65 #DROPGSW_O = dropgsw.o
66 #DROPRSS_O = dropgsw.o
68 # provide mysql function
69 #include Makefile34m.common_sql
72 include Makefile34m.common