2 # makefile for fasta3, fasta3_t. Use makefile.pvm for pvcompxx.
5 # Dec 8, 2005 - with gcc4.0.2 (or .1) under Redhat Linux Fedora FC4 -03 breaks the alignment code
8 CC= gcc -g -O -DSW_SSE2 -msse2
9 #CC = gcc -g -DDEBUG -DSW_SSE2 -msse2
11 #CC=gcc -Wall -pedantic -ansi -g -O
12 #CC= /usr/local/parasoft/bin/insure -g -DDEBUG
14 # EBI uses the following with pgcc, -O3 does not work:
15 # CC= pgcc -O2 -pipe -mcpu=pentiumpro -march=pentiumpro -fomit-frame-pointer
17 # this file works for x86 LINUX
20 CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="':'" -c -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"your_fasta_host_here"' -DUSE_MMAP -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC
22 # use options below for superfamily validations
23 #CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="'|'" -c -DMAX_WORKERS=4 -DTHR_EXIT=pthread_exit -DPROGRESS -DSUPERFAMNUM -DUSE_MMAP -D_REENTRANT -DBIG_LIB64 -D_LARGE_FILE_SOURCE -DUSE_FSEEKO -D_FILE_OFFSET_BITS=64 -DHAS_INTTYPES -DSAMP_STATS
25 # -I/usr/local/include/mysql -DMYSQL_DB
27 #(for mySQL databases) (also requires change to Makefile34.common)
30 #LIB_M = -L/usr/local/lib/mysql -lmysqlclient -lm
44 DROPNFA_O = drop_nfa.o
45 DROPTFA_O = drop_tfa.o
46 DROPGSW_O = dropgsw.o smith_waterman_sse2.o
47 DROPRSS_O = dropgsw.o smith_waterman_sse2.o
49 # renamed (fasta33) programs
50 include Makefile34m.common
51 # conventional (fasta3) names
52 # include Makefile.common