# $Name:  $ - $Id: Makefile.pLinux 488 2011-01-21 17:38:53Z wrp $
#
# makefile for fasta3, fasta3_t.  Use makefile.pvm for pvcompxx.
# this file works for DEC Alphas
#
# this file supports mmap()'ed databases in BLAST2 format use -DUSE_MMAP
# for mmap()ed BLAST2 format.

# the -DDEBUG option provides additional debugging information, particularly
# with -D on the command line.

# use -DBIG_LIB64 to generate and use 64-bit offsets in map_db .xin
# files

# for Tru64 4.0F, no "<inttypes.h>" 4.0G has inttypes.h

CC= xlc_r

#CC= cc -g3 -O -std1
#CC= insure -g -DDEBUG
#CC= cc -g -DDEBUG -std1

#CC= gcc -g -Wall
#
# standard line for normal searching
CFLAGS= -O3 -qtune=auto -qarch=auto -DUNIX -DTIMES -DBIGMEM -DMAX_WORKERS=4 -DSFCHAR="':'" -DTHR_EXIT=pthread_exit  -DUSE_MMAP -DIS_BIG_ENDIAN -DSAMP_STATS -DPGM_DOC -D_LARGE_FILES -DHAS_INTTYPES -D__pLinux__ -DBIG_LIB64
#
#(-DMYSQL_DB for mySQL databases)  (also requires change to Makefile35.common)

# special options for SUPERFAMLIES
#CFLAGS= -DM10_CONS -DUNIX -DTIMES -DHZ=60 -DBIGMEM -DSFCHAR="'|'" -DMAX_WORKERS=4 -DTHR_EXIT=pthread_exit -DPROGRESS -DSUPERFAMNUM -DIS_LITTLE_ENDIAN -DUSE_MMAP -DMAXBEST=200000
 
LIB_M = -lm
#LIB_M = -L/usr/local/lib/mysql -lmysqlclient -lm
# for mySQL databases

HFLAGS= -o
NFLAGS= -o

#for DEC Unix V4.0 
#THR_SUBS = pthr_subs2
#THR_LIBS = -lpthreads
#THR_CC =

#for Sun
#THR_SUBS = uthr_subs
#THR_LIBS = -lthread
#THR_CC =
#
# for SGI with current pthreads
#THR_SUBS = pthr_subs
#THR_LIBS = -lpthreads
#THR_CC = 
#
# for IBM with current pthreads
#CC= xlc_r -v -g
#THR_SUBS = ibm_pthr_subs
#THR_LIBS = -lpthreads
#THR_CC =


# for IBM Linux with current pthreads
THR_SUBS = pthr_subs2
THR_LIBS = -lpthread

BIN = ../bin
XDIR = /seqprg/slib/bin

# set up files for SSE2/Altivec acceleration
#
include ../make/Makefile.sse_alt

# no acceleration
#
DROPGSW_O = $(DROPGSW_NA_O)
DROPLAL_O = $(DROPLAL_NA_O)
DROPGNW_O = $(DROPGNW_NA_O)
DROPLNW_O = $(DROPLNW_NA_O)

# renamed (fasta34)  programs
#include ../make/Makefile36m.common_sql
include ../make/Makefile36m.common

