Attachment #62215 for bug #93052




# ex:ts=8
# New ports collection makefile for:	fasta3
# Date created:		29 January 2001
# Whom:	      		Johann Visagie <johann@egenetics.com>

#

PORTNAME=	fasta3
PORTVERSION=	34.t25.d4
CATEGORIES=	biology
MASTER_SITES=	ftp://ftp.virginia.edu/pub/fasta/
DISTNAME=	fasta${PORTVERSION:S/.//g}
EXTRACT_SUFX=	.shar.Z

MAINTAINER=	fernan@iib.unsam.edu.ar
COMMENT=	A collection of programs for searching DNA and protein databases

NO_CDROM=	"May not be sold or incorporated into a commercial product"
WRKSRC=		${WRKDIR}/${PORTNAME}
SUB_FILES=	pkg-message

FASTA3_DOCS=	README COPYRIGHT FASTA_LIST fasta3x.me fasta3x.doc \
		fasta20.doc fasta_func.doc readme.* fasta.defaults
DATA=		*.mat
EXAMPLES=	*.aa *.lc *.seq

MAN1=		fasta3.1 fastf3.1 fasts3.1 map_db.1 prss3.1
MLINKS=		fasta3.1 tfasta3.1 fasta3.1 fastx3.1  fasta3.1 tfastx3.1  \

	done

post-install:
	${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample
	@ ${MKDIR} ${DATADIR}
.for data in ${DATA}
	${INSTALL_DATA} ${WRKSRC}/${data} ${DATADIR}
.endfor
	@ ${MKDIR} ${EXAMPLESDIR}
.for ex in ${EXAMPLES}
	${INSTALL_DATA} ${WRKSRC}/${ex} ${EXAMPLESDIR}
.endfor
.for manpage in ${MAN1}
	@ ${INSTALL_MAN} ${WRKSRC}/${manpage} ${MAN1PREFIX}/man/man1/
.endfor
.if !defined(NOPORTDOCS)
	@ ${MKDIR} ${DOCSDIR}
.for docfile in ${FASTA3_DOCS}
	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR}
.endfor
.endif
.if !defined(BATCH)
	@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#' ${.CURDIR}/pkg-message > ${PKGMESSAGE}
	@ ${CAT} ${PKGMESSAGE}
.endif

.include <bsd.port.mk>

Lines 1-3 Link Here

(-)fasta3/distinfo (-3 / +3 lines)
1	MD5 (fasta33t08d4.shar.Z) = e6217268e122b2ca7c51b443425e40e3	1	MD5 (fasta34t25d4.shar.Z) = 554190cb7bf2488150a96e309651e9c7
2	SHA256 (fasta33t08d4.shar.Z) = f2eb329393cd330c6848cff2a147fcc2c2f74dff6033cf7ba70177ab4bcca231	2	SHA256 (fasta34t25d4.shar.Z) = 4d901bc738074c6c72d568b3852cf7e8a91a71ca25a1b2d74b8b1ae997d956fe
3	SIZE (fasta33t08d4.shar.Z) = 685912	3	SIZE (fasta34t25d4.shar.Z) = 799416




--- Makefile.orig	Sat Feb  4 21:12:38 2006
+++ Makefile	Sat Feb  4 21:15:12 2006
@@ -7,7 +7,7 @@
 # in dropnfa.c  (wrp 3/19/1998)
 # use -DBIG_LIB64 to generate 64-bit offsets in map_db .xin files
 
-CC= cc -O -std1
+#CC= cc -O -std1
 #CC= insure -g -DDEBUG
 #CC= cc -g -DDEBUG -std1
 #CC= gcc -g -Wall
 #
 # standard line for normal searching
-CFLAGS= -DM10_CONS -DUNIX -DTIMES -DHZ=60 -DBIGMEM -DMAX_WORKERS=4 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"fasta.bioch.virginia.edu/fasta/cgi"' -DIS_LITTLE_ENDIAN -DUSE_MMAP
+CFLAGS+= -DM10_CONS -DUNIX -DTIMES -DHZ=60 -DBIGMEM -DMAX_WORKERS=4 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"fasta.bioch.virginia.edu/fasta/cgi"' -DIS_LITTLE_ENDIAN -DUSE_MMAP
 # -I/usr/local/include/mysql -DMYSQL_DB 
 #(for mySQL databases)  (also requires change to Makefile33.common)
 
@@ -32,11 +32,15 @@
 HFLAGS= -o
 NFLAGS= -o
 
-CC= gcc -g -O3
+#CC= gcc -g -O3
 #CC=gcc -Wall -pedantic -ansi -g -O
 #CC = gcc -g -DDEBUG
 #CC= /opt/parasoft/bin.linux2/insure -g -pg -DDEBUG
@@ -21,7 +21,7 @@
 #CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="'|'" -c -DMAX_WORKERS=2 -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
 
 # standard options
-CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="':'" -c -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"wrpx00.bioch.virginia.edu/fasta/cgi"' -DUSE_MMAP -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC
+CFLAGS+= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="':'" -c -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"wrpx00.bioch.virginia.edu/fasta/cgi"' -DUSE_MMAP -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC
 # -I/usr/local/include/mysql -DMYSQL_DB 
 #
 #(for mySQL databases)  (also requires change to Makefile34.common)
@@ -38,7 +38,7 @@
 THR_LIBS = -lpthread
 THR_CC =
 
-XDIR = /seqprg/bin
+#THR_SUBS = pthr_subs
+#THR_LIBS = -threads
+#THR_CC =
+#
 #for Sun
 #THR_SUBS = uthr_subs
 #THR_LIBS = -lthread
@@ -53,9 +57,9 @@
 #THR_LIBS = -lpthreads
 #THR_CC =
 
-XDIR = /seqprg/slib/bin
+XDIR = ${PREFIX}/bin
 
 DROPNFA_O = drop_nfa.o
 DROPGSW_O = dropgsw.o
+#include Makefile33.common
 # conventional (fasta3) names
-#include Makefile.common
+include Makefile.common




--- Makefile.common.orig	Mon Jan 29 12:42:32 2001
+++ Makefile.common	Mon Jan 29 13:44:06 2001
@@ -46,7 +46,7 @@
 XTPROGS = fastx33_t tfastx33_t fasty33_t tfasty33_t
 XPROGS = fastx33 tfastx33  fasty33 tfasty33
 
-PROGS = $(SPROGS) $(TPROGS)
+PROGS = $(SPROGS) $(TPROGS) $(APROGS) $(XTPROGS) $(XPROGS)
 
 all : $(PROGS)
 
@@ -60,7 +60,7 @@
 	rm -f *.o $(PROGS)
 
 install:
-	cp $(PROGS) $(XDIR)
+	$(BSD_INSTALL_PROGRAM) $(PROGS) $(XDIR)
 
 sinstall:
 	cp $(SPROGS) $(XDIR)

Lines 1-11 Link Here

(-)fasta3/files/patch-comp_thr.c (-11 lines)
1	--- comp_thr.c.orig Thu Aug 22 20:32:10 2002
2	+++ comp_thr.c Thu Aug 22 20:32:25 2002
3	@@ -16,7 +16,7 @@
4	#include <time.h>
5
6	#ifdef UNIX
7	-#if !defined(__NetBSD__) && !defined(MacOSX)
8	+#if !defined(__FreeBSD__) && !defined(__NetBSD__) && !defined(MacOSX)
9	#include <values.h>
10	#else
11	#include <limits.h>

Lines 1-11 Link Here

(-)fasta3/files/patch-compacc.c (-11 lines)
1	--- compacc.c.orig Thu Aug 22 20:30:30 2002
2	+++ compacc.c Thu Aug 22 20:30:43 2002
3	@@ -11,7 +11,7 @@
4	#if defined(UNIX) \|\| defined(MSDOS)
5	#include <sys/types.h>
6	#endif
7	-#if !defined(__MWERKS__) && !defined(MacOSX)
8	+#if !defined(__FreeBSD__) && !defined(__MWERKS__) && !defined(MacOSX)
9	#include <values.h>
10	#else
11	#include <limits.h>

Lines 1-11 Link Here

(-)fasta3/files/patch-complib.c (-11 lines)
1	--- complib.c.orig Thu Aug 22 20:33:57 2002
2	+++ complib.c Thu Aug 22 20:34:07 2002
3	@@ -29,7 +29,7 @@
4	#include <ctype.h>
5	#include <time.h>
6	#ifdef UNIX
7	-#if !defined(__NetBSD__) && !defined(MacOSX)
8	+#if !defined(__FreeBSD__) && !defined(__NetBSD__) && !defined(MacOSX)
9	#include <values.h>
10	#else
11	#include <limits.h>

Lines 1-11 Link Here

(-)fasta3/files/patch-scaleswn.c (-11 lines)
1	--- scaleswn.c.orig Thu Aug 22 20:30:55 2002
2	+++ scaleswn.c Thu Aug 22 20:31:06 2002
3	@@ -26,7 +26,7 @@
4	#include <math.h>
5	#include <string.h>
6
7	-#if !defined(__MWERKS__) && !defined(MacOSX)
8	+#if !defined(__FreeBSD__) && !defined(__MWERKS__) && !defined(MacOSX)
9	#include <values.h>
10	#else
11	#include <limits.h> /* needed for LONG_MAX */




=============================================================================

 The FASTA3 package has been successfully installed.

 A sample configuration file has been installed to 
 %%PREFIX%%/etc 
 as "fastlibs.sample". This may be renamed to "fastlibs" and edited
 to suit the requirements of a particular site.

 In order to use the FASTA3 programs, a user must set the environment
 variable FASTLIBS to contain the full path of the FASTA3 configuration
 file, e.g.:

 set FASTLIBS to: "%%PREFIX%%/etc/fastlibs"

==============================================================================




--------------------------------------------------------------------------

The FASTA3 package has been successfully installed.

NB:  A sample configuration file has been installed to %%PREFIX%%/etc as
"fastlibs.sample".  This may be renamed to "fastlibs" and edited
to suit the requirements of a particular site.

In order to use the FASTA3 programs, a user must set the environment
variable FASTLIBS to contain the full path of the FASTA3 configuration
file, e.g.:

- set FASTLIBS to:  "%%PREFIX%%/etc/fastlibs"

--------------------------------------------------------------------------




bin/fasta34
bin/prss34_t
bin/tfastf34_t
bin/fastf34_t
bin/fastm34_t
bin/tfasts34_t
bin/tfasty34_t
bin/fasty34_t
bin/tfastx34_t
bin/fastx34_t
bin/tfasta34_t
bin/fasts34_t
bin/fasta34_t
bin/ssearch34_t
bin/tfastf34
bin/fastf34
bin/prfx34
bin/prss34
bin/tfastm34
bin/fastm34
bin/tfasts34
bin/tfasty34
bin/fasty34
bin/tfastx34
bin/fastx34
bin/fasts34
bin/tfasta34
bin/ssearch34
bin/prfx34_t
etc/fastlibs.sample
%%PORTDOCS%%%%DOCSDIR%%/README
%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
%%PORTDOCS%%%%DOCSDIR%%/FASTA_LIST
%%PORTDOCS%%%%DOCSDIR%%/fasta3x.me
%%PORTDOCS%%%%DOCSDIR%%/fasta3x.doc
%%PORTDOCS%%%%DOCSDIR%%/fasta20.doc
%%PORTDOCS%%%%DOCSDIR%%/fasta_func.doc
%%PORTDOCS%%%%DOCSDIR%%/readme.mpi_3.3
%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_2.0
%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.0
%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.2
%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.3
%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.4

%%PORTDOCS%%%%DOCSDIR%%/readme.v31t1
%%PORTDOCS%%%%DOCSDIR%%/readme.v32t0
%%PORTDOCS%%%%DOCSDIR%%/readme.v33t0
%%PORTDOCS%%%%DOCSDIR%%/readme.v34t0
%%PORTDOCS%%%%DOCSDIR%%/readme.w32
%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
%%EXAMPLESDIR%%/egmsmg.aa
%%EXAMPLESDIR%%/gtm1_human.aa
%%EXAMPLESDIR%%/gtt1_drome.aa
%%EXAMPLESDIR%%/h10_human.aa
%%EXAMPLESDIR%%/hahu.aa
%%EXAMPLESDIR%%/lcbo.aa
%%EXAMPLESDIR%%/m1r.aa
%%EXAMPLESDIR%%/m2.aa
%%EXAMPLESDIR%%/mchu.aa
%%EXAMPLESDIR%%/mgstm1.aa
%%EXAMPLESDIR%%/ms1.aa
%%EXAMPLESDIR%%/musplfm.aa
%%EXAMPLESDIR%%/mwkw.aa
%%EXAMPLESDIR%%/mwrtc1.aa
%%EXAMPLESDIR%%/n0.aa
%%EXAMPLESDIR%%/n1.aa
%%EXAMPLESDIR%%/n2.aa
%%EXAMPLESDIR%%/n2s.aa
%%EXAMPLESDIR%%/n2t.aa
%%EXAMPLESDIR%%/ngt.aa
%%EXAMPLESDIR%%/ngts.aa
%%EXAMPLESDIR%%/oohu.aa
%%EXAMPLESDIR%%/prio_atepa.aa
%%EXAMPLESDIR%%/qrhuld.aa
%%EXAMPLESDIR%%/xurt8c.aa
%%EXAMPLESDIR%%/xurtg.aa
%%EXAMPLESDIR%%/mgstm1.lc
%%EXAMPLESDIR%%/xurt8c.lc
%%EXAMPLESDIR%%/bovgh.seq
%%EXAMPLESDIR%%/bovprl.seq
%%EXAMPLESDIR%%/gst.seq
%%EXAMPLESDIR%%/hsgstm1b.seq
%%EXAMPLESDIR%%/humgstd.seq
%%EXAMPLESDIR%%/mgstm1.seq
%%EXAMPLESDIR%%/mgtt2_x.seq
%%DATADIR%%/blosum45.mat
%%DATADIR%%/blosum50.mat
%%DATADIR%%/blosum62.mat
%%DATADIR%%/blosum80.mat
%%DATADIR%%/dna.mat
%%DATADIR%%/idn_aa.mat
%%DATADIR%%/md_10.mat
%%DATADIR%%/md_20.mat
%%DATADIR%%/md_40.mat
%%DATADIR%%/pam120.mat
%%DATADIR%%/pam250.mat
%%DATADIR%%/rna.mat
%%DATADIR%%/vtml160.mat
%%PORTDOCS%%@dirrm %%DOCSDIR%%
@dirrm %%EXAMPLESDIR%%
@dirrm %%DATADIR%%

Return to bug 93052

Lines 1-3 Link Here

(-)fasta3/Makefile (-14 / +22 lines)
		1	# ex:ts=8
1	# New ports collection makefile for: fasta3	2	# New ports collection makefile for: fasta3
2	# Date created: 29 January 2001	3	# Date created: 29 January 2001
3	# Whom: Johann Visagie <johann@egenetics.com>	4	# Whom: Johann Visagie <johann@egenetics.com>
Lines 6-26 Link Here
6	#	7	#
7		8
8	PORTNAME= fasta3	9	PORTNAME= fasta3
9	PORTVERSION= 33.t08.d4	10	PORTVERSION= 34.t25.d4
10	CATEGORIES= biology	11	CATEGORIES= biology
11	MASTER_SITES= ftp://ftp.virginia.edu/pub/fasta/	12	MASTER_SITES= ftp://ftp.virginia.edu/pub/fasta/
12	DISTNAME= fasta${PORTVERSION:S/.//g}	13	DISTNAME= fasta${PORTVERSION:S/.//g}
13	EXTRACT_SUFX= .shar.Z	14	EXTRACT_SUFX= .shar.Z
14		15
15	MAINTAINER= fernan@iib.unsam.edu.ar	16	MAINTAINER= fernan@iib.unsam.edu.ar
16	COMMENT= A collection of programs for searching DNA and protein databases, v3	17	COMMENT= A collection of programs for searching DNA and protein databases
17		18
18	NO_CDROM= May not be sold or incorporated into a commercial product	19	NO_CDROM= "May not be sold or incorporated into a commercial product"
19	WRKSRC= ${WRKDIR}/fasta3	20	WRKSRC= ${WRKDIR}/${PORTNAME}
20	PKGMESSAGE= ${WRKDIR}/pkg-message	21	SUB_FILES= pkg-message
21	FASTA3_DOCDIR= ${PREFIX}/share/doc/fasta3	22
22	FASTA3_DOCS= 00README.1st README COPYRIGHT fasta3x.me fasta3x.doc \	23	FASTA3_DOCS= README COPYRIGHT FASTA_LIST fasta3x.me fasta3x.doc \
23	readme.*	24	fasta20.doc fasta_func.doc readme.* fasta.defaults
		25	DATA= *.mat
		26	EXAMPLES= .aa .lc *.seq
24		27
25	MAN1= fasta3.1 fastf3.1 fasts3.1 map_db.1 prss3.1	28	MAN1= fasta3.1 fastf3.1 fasts3.1 map_db.1 prss3.1
26	MLINKS= fasta3.1 tfasta3.1 fasta3.1 fastx3.1 fasta3.1 tfastx3.1 \	29	MLINKS= fasta3.1 tfasta3.1 fasta3.1 fastx3.1 fasta3.1 tfastx3.1 \
Lines 35-53 Link Here
35	done	38	done
36		39
37	post-install:	40	post-install:
38	@ ${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample	41	${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample
		42	@ ${MKDIR} ${DATADIR}
		43	.for data in ${DATA}
		44	${INSTALL_DATA} ${WRKSRC}/${data} ${DATADIR}
		45	.endfor
		46	@ ${MKDIR} ${EXAMPLESDIR}
		47	.for ex in ${EXAMPLES}
		48	${INSTALL_DATA} ${WRKSRC}/${ex} ${EXAMPLESDIR}
		49	.endfor
39	.for manpage in ${MAN1}	50	.for manpage in ${MAN1}
40	@ ${INSTALL_MAN} ${WRKSRC}/${manpage} ${MAN1PREFIX}/man/man1/	51	@ ${INSTALL_MAN} ${WRKSRC}/${manpage} ${MAN1PREFIX}/man/man1/
41	.endfor	52	.endfor
42	.if !defined(NOPORTDOCS)	53	.if !defined(NOPORTDOCS)
43	@ ${MKDIR} ${FASTA3_DOCDIR}	54	@ ${MKDIR} ${DOCSDIR}
44	.for docfile in ${FASTA3_DOCS}	55	.for docfile in ${FASTA3_DOCS}
45	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${FASTA3_DOCDIR}	56	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR}
46	.endfor	57	.endfor
47	.endif	58	.endif
48	.if !defined(BATCH)
49	@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#' ${.CURDIR}/pkg-message > ${PKGMESSAGE}
50	@ ${CAT} ${PKGMESSAGE}	59	@ ${CAT} ${PKGMESSAGE}
51	.endif
52		60
53	.include <bsd.port.mk>	61	.include <bsd.port.mk>

Lines 1-49 Link Here

(-)fasta3/files/patch-Makefile (-43 / +23 lines)
1	--- Makefile.orig Mon May 7 11:36:23 2001	1	--- Makefile.orig Sat Feb 4 21:12:38 2006
2	+++ Makefile Mon May 7 11:40:36 2001	2	+++ Makefile Sat Feb 4 21:15:12 2006
3	@@ -12,13 +12,13 @@	3	@@ -7,7 +7,7 @@
4		4	# in dropnfa.c (wrp 3/19/1998)
5	# use -DBIG_LIB64 to generate 64-bit offsets in map_db .xin files
6
7	-CC= cc -O -std1
8	+#CC= cc -O -std1
9	#CC= insure -g -DDEBUG
10	#CC= cc -g -DDEBUG -std1
11	#CC= gcc -g -Wall
12	#	5	#
13	# standard line for normal searching
14	-CFLAGS= -DM10_CONS -DUNIX -DTIMES -DHZ=60 -DBIGMEM -DMAX_WORKERS=4 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"fasta.bioch.virginia.edu/fasta/cgi"' -DIS_LITTLE_ENDIAN -DUSE_MMAP
15	+CFLAGS+= -DM10_CONS -DUNIX -DTIMES -DHZ=60 -DBIGMEM -DMAX_WORKERS=4 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"fasta.bioch.virginia.edu/fasta/cgi"' -DIS_LITTLE_ENDIAN -DUSE_MMAP
16	# -I/usr/local/include/mysql -DMYSQL_DB
17	#(for mySQL databases) (also requires change to Makefile33.common)
18
19	@@ -32,11 +32,15 @@
20	HFLAGS= -o
21	NFLAGS= -o
22		6
23	-#for DEC Unix V4.0	7	-CC= gcc -g -O3
24	THR_SUBS = pthr_subs	8	+#CC= gcc -g -O3
25	-THR_LIBS = -threads	9	#CC=gcc -Wall -pedantic -ansi -g -O
26	+THR_LIBS = -pthread	10	#CC = gcc -g -DDEBUG
		11	#CC= /opt/parasoft/bin.linux2/insure -g -pg -DDEBUG
		12	@@ -21,7 +21,7 @@
		13	#CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="'\|'" -c -DMAX_WORKERS=2 -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
		14
		15	# standard options
		16	-CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="':'" -c -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"wrpx00.bioch.virginia.edu/fasta/cgi"' -DUSE_MMAP -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC
		17	+CFLAGS+= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="':'" -c -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"wrpx00.bioch.virginia.edu/fasta/cgi"' -DUSE_MMAP -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC
		18	# -I/usr/local/include/mysql -DMYSQL_DB
		19	#
		20	#(for mySQL databases) (also requires change to Makefile34.common)
		21	@@ -38,7 +38,7 @@
		22	THR_LIBS = -lpthread
27	THR_CC =	23	THR_CC =
28		24
29	+#for DEC Unix V4.0	25	-XDIR = /seqprg/bin
30	+#THR_SUBS = pthr_subs
31	+#THR_LIBS = -threads
32	+#THR_CC =
33	+#
34	#for Sun
35	#THR_SUBS = uthr_subs
36	#THR_LIBS = -lthread
37	@@ -53,9 +57,9 @@
38	#THR_LIBS = -lpthreads
39	#THR_CC =
40
41	-XDIR = /seqprg/slib/bin
42	+XDIR = ${PREFIX}/bin	26	+XDIR = ${PREFIX}/bin
43		27
44	# renamed (fasta33) programs	28	DROPNFA_O = drop_nfa.o
45	-include Makefile33.common	29	DROPGSW_O = dropgsw.o
46	+#include Makefile33.common
47	# conventional (fasta3) names
48	-#include Makefile.common
49	+include Makefile.common

Lines 1-20 Link Here

(-)fasta3/files/patch-Makefile.common (-20 lines)
1	--- Makefile.common.orig Mon Jan 29 12:42:32 2001
2	+++ Makefile.common Mon Jan 29 13:44:06 2001
3	@@ -46,7 +46,7 @@
4	XTPROGS = fastx33_t tfastx33_t fasty33_t tfasty33_t
5	XPROGS = fastx33 tfastx33 fasty33 tfasty33
6
7	-PROGS = $(SPROGS) $(TPROGS)
8	+PROGS = $(SPROGS) $(TPROGS) $(APROGS) $(XTPROGS) $(XPROGS)
9
10	all : $(PROGS)
11
12	@@ -60,7 +60,7 @@
13	rm -f *.o $(PROGS)
14
15	install:
16	- cp $(PROGS) $(XDIR)
17	+ $(BSD_INSTALL_PROGRAM) $(PROGS) $(XDIR)
18
19	sinstall:
20	cp $(SPROGS) $(XDIR)

Line 0 Link Here

(-)fasta3/files/pkg-message.in (+16 lines)
	1	=============================================================================
	2
	3	The FASTA3 package has been successfully installed.
	4
	5	A sample configuration file has been installed to
	6	%%PREFIX%%/etc
	7	as "fastlibs.sample". This may be renamed to "fastlibs" and edited
	8	to suit the requirements of a particular site.
	9
	10	In order to use the FASTA3 programs, a user must set the environment
	11	variable FASTLIBS to contain the full path of the FASTA3 configuration
	12	file, e.g.:
	13
	14	set FASTLIBS to: "%%PREFIX%%/etc/fastlibs"
	15
	16	==============================================================================

Lines 1-15 Link Here

(-)fasta3/pkg-message (-15 lines)
1	--------------------------------------------------------------------------
2
3	The FASTA3 package has been successfully installed.
4
5	NB: A sample configuration file has been installed to %%PREFIX%%/etc as
6	"fastlibs.sample". This may be renamed to "fastlibs" and edited
7	to suit the requirements of a particular site.
8
9	In order to use the FASTA3 programs, a user must set the environment
10	variable FASTLIBS to contain the full path of the FASTA3 configuration
11	file, e.g.:
12
13	- set FASTLIBS to: "%%PREFIX%%/etc/fastlibs"
14
15	--------------------------------------------------------------------------

Lines 1-11 Link Here

(-)fasta3/pkg-plist (-30 / +87 lines)
1	%%PORTDOCS%%%%DOCSDIR%%/00README.1st	1	bin/fasta34
2	%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT	2	bin/prss34_t
		3	bin/tfastf34_t
		4	bin/fastf34_t
		5	bin/fastm34_t
		6	bin/tfasts34_t
		7	bin/tfasty34_t
		8	bin/fasty34_t
		9	bin/tfastx34_t
		10	bin/fastx34_t
		11	bin/tfasta34_t
		12	bin/fasts34_t
		13	bin/fasta34_t
		14	bin/ssearch34_t
		15	bin/tfastf34
		16	bin/fastf34
		17	bin/prfx34
		18	bin/prss34
		19	bin/tfastm34
		20	bin/fastm34
		21	bin/tfasts34
		22	bin/tfasty34
		23	bin/fasty34
		24	bin/tfastx34
		25	bin/fastx34
		26	bin/fasts34
		27	bin/tfasta34
		28	bin/ssearch34
		29	bin/prfx34_t
		30	etc/fastlibs.sample
3	%%PORTDOCS%%%%DOCSDIR%%/README	31	%%PORTDOCS%%%%DOCSDIR%%/README
4	%%PORTDOCS%%%%DOCSDIR%%/fasta3x.doc	32	%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
		33	%%PORTDOCS%%%%DOCSDIR%%/FASTA_LIST
5	%%PORTDOCS%%%%DOCSDIR%%/fasta3x.me	34	%%PORTDOCS%%%%DOCSDIR%%/fasta3x.me
		35	%%PORTDOCS%%%%DOCSDIR%%/fasta3x.doc
		36	%%PORTDOCS%%%%DOCSDIR%%/fasta20.doc
		37	%%PORTDOCS%%%%DOCSDIR%%/fasta_func.doc
6	%%PORTDOCS%%%%DOCSDIR%%/readme.mpi_3.3	38	%%PORTDOCS%%%%DOCSDIR%%/readme.mpi_3.3
7	%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_2.0
8	%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.0
9	%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.2	39	%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.2
10	%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.3	40	%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.3
11	%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.4	41	%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.4
Lines 16-45 Link Here
16	%%PORTDOCS%%%%DOCSDIR%%/readme.v31t1	46	%%PORTDOCS%%%%DOCSDIR%%/readme.v31t1
17	%%PORTDOCS%%%%DOCSDIR%%/readme.v32t0	47	%%PORTDOCS%%%%DOCSDIR%%/readme.v32t0
18	%%PORTDOCS%%%%DOCSDIR%%/readme.v33t0	48	%%PORTDOCS%%%%DOCSDIR%%/readme.v33t0
		49	%%PORTDOCS%%%%DOCSDIR%%/readme.v34t0
19	%%PORTDOCS%%%%DOCSDIR%%/readme.w32	50	%%PORTDOCS%%%%DOCSDIR%%/readme.w32
20	bin/fasta3	51	%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
21	bin/fasta3_t	52	%%EXAMPLESDIR%%/egmsmg.aa
22	bin/fastf3	53	%%EXAMPLESDIR%%/gtm1_human.aa
23	bin/fastf3_t	54	%%EXAMPLESDIR%%/gtt1_drome.aa
24	bin/fasts3	55	%%EXAMPLESDIR%%/h10_human.aa
25	bin/fasts3_t	56	%%EXAMPLESDIR%%/hahu.aa
26	bin/fastx3	57	%%EXAMPLESDIR%%/lcbo.aa
27	bin/fastx3_t	58	%%EXAMPLESDIR%%/m1r.aa
28	bin/fasty3	59	%%EXAMPLESDIR%%/m2.aa
29	bin/fasty3_t	60	%%EXAMPLESDIR%%/mchu.aa
30	bin/map_db	61	%%EXAMPLESDIR%%/mgstm1.aa
31	bin/prss3	62	%%EXAMPLESDIR%%/ms1.aa
32	bin/ssearch3	63	%%EXAMPLESDIR%%/musplfm.aa
33	bin/ssearch3_t	64	%%EXAMPLESDIR%%/mwkw.aa
34	bin/tfasta3	65	%%EXAMPLESDIR%%/mwrtc1.aa
35	bin/tfasta3_t	66	%%EXAMPLESDIR%%/n0.aa
36	bin/tfastf3	67	%%EXAMPLESDIR%%/n1.aa
37	bin/tfastf3_t	68	%%EXAMPLESDIR%%/n2.aa
38	bin/tfasts3	69	%%EXAMPLESDIR%%/n2s.aa
39	bin/tfasts3_t	70	%%EXAMPLESDIR%%/n2t.aa
40	bin/tfastx3	71	%%EXAMPLESDIR%%/ngt.aa
41	bin/tfastx3_t	72	%%EXAMPLESDIR%%/ngts.aa
42	bin/tfasty3	73	%%EXAMPLESDIR%%/oohu.aa
43	bin/tfasty3_t	74	%%EXAMPLESDIR%%/prio_atepa.aa
44	etc/fastlibs.sample	75	%%EXAMPLESDIR%%/qrhuld.aa
		76	%%EXAMPLESDIR%%/xurt8c.aa
		77	%%EXAMPLESDIR%%/xurtg.aa
		78	%%EXAMPLESDIR%%/mgstm1.lc
		79	%%EXAMPLESDIR%%/xurt8c.lc
		80	%%EXAMPLESDIR%%/bovgh.seq
		81	%%EXAMPLESDIR%%/bovprl.seq
		82	%%EXAMPLESDIR%%/gst.seq
		83	%%EXAMPLESDIR%%/hsgstm1b.seq
		84	%%EXAMPLESDIR%%/humgstd.seq
		85	%%EXAMPLESDIR%%/mgstm1.seq
		86	%%EXAMPLESDIR%%/mgtt2_x.seq
		87	%%DATADIR%%/blosum45.mat
		88	%%DATADIR%%/blosum50.mat
		89	%%DATADIR%%/blosum62.mat
		90	%%DATADIR%%/blosum80.mat
		91	%%DATADIR%%/dna.mat
		92	%%DATADIR%%/idn_aa.mat
		93	%%DATADIR%%/md_10.mat
		94	%%DATADIR%%/md_20.mat
		95	%%DATADIR%%/md_40.mat
		96	%%DATADIR%%/pam120.mat
		97	%%DATADIR%%/pam250.mat
		98	%%DATADIR%%/rna.mat
		99	%%DATADIR%%/vtml160.mat
45	%%PORTDOCS%%@dirrm %%DOCSDIR%%	100	%%PORTDOCS%%@dirrm %%DOCSDIR%%
		101	@dirrm %%EXAMPLESDIR%%
		102	@dirrm %%DATADIR%%