View | Details | Raw Unified | Return to bug 93052 | Differences between
and this patch

Collapse All | Expand All

(-)fasta3/Makefile (-14 / +24 lines)
Lines 1-3 Link Here
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=	${PREFIX}/share/doc/fasta3
22
22
FASTA3_DOCS=	00README.1st README COPYRIGHT fasta3x.me fasta3x.doc \
23
MAKE_ENV+=	THR_LIBS=${PTHREAD_LIBS}
23
		readme.*
24
25
FASTA3_DOCS=	README COPYRIGHT FASTA_LIST fasta3x.me fasta3x.doc \
26
		fasta20.doc fasta_func.doc readme.* fasta.defaults
27
DATA=		*.mat
28
EXAMPLES=	*.aa *.lc *.seq
24
29
25
MAN1=		fasta3.1 fastf3.1 fasts3.1 map_db.1 prss3.1
30
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  \
31
MLINKS=		fasta3.1 tfasta3.1 fasta3.1 fastx3.1  fasta3.1 tfastx3.1  \
Lines 35-53 Link Here
35
	done
40
	done
36
41
37
post-install:
42
post-install:
38
	@ ${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample
43
	${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample
44
	@ ${MKDIR} ${DATADIR}
45
.for data in ${DATA}
46
	${INSTALL_DATA} ${WRKSRC}/${data} ${DATADIR}
47
.endfor
48
	@ ${MKDIR} ${EXAMPLESDIR}
49
.for ex in ${EXAMPLES}
50
	${INSTALL_DATA} ${WRKSRC}/${ex} ${EXAMPLESDIR}
51
.endfor
39
.for manpage in ${MAN1}
52
.for manpage in ${MAN1}
40
	@ ${INSTALL_MAN} ${WRKSRC}/${manpage} ${MAN1PREFIX}/man/man1/
53
	@ ${INSTALL_MAN} ${WRKSRC}/${manpage} ${MAN1PREFIX}/man/man1/
41
.endfor
54
.endfor
42
.if !defined(NOPORTDOCS)
55
.if !defined(NOPORTDOCS)
43
	@ ${MKDIR} ${FASTA3_DOCDIR}
56
	@ ${MKDIR} ${DOCSDIR}
44
.for docfile in ${FASTA3_DOCS}
57
.for docfile in ${FASTA3_DOCS}
45
	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${FASTA3_DOCDIR}
58
	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR}
46
.endfor
59
.endfor
47
.endif
60
.endif
48
.if !defined(BATCH)
49
	@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#' ${.CURDIR}/pkg-message > ${PKGMESSAGE}
50
	@ ${CAT} ${PKGMESSAGE}
61
	@ ${CAT} ${PKGMESSAGE}
51
.endif
52
62
53
.include <bsd.port.mk>
63
.include <bsd.port.mk>
(-)fasta3/distinfo (-3 / +3 lines)
Lines 1-3 Link Here
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
(-)fasta3/files/patch-Makefile (-42 / +26 lines)
Lines 1-49 Link Here
1
--- Makefile.orig	Mon May  7 11:36:23 2001
1
--- Makefile.orig	Thu Feb  9 12:03:37 2006
2
+++ Makefile	Mon May  7 11:40:36 2001
2
+++ Makefile	Thu Feb  9 12:07:21 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
 
6
 
19
@@ -32,11 +32,15 @@
7
-CC= gcc -g -O3
20
 HFLAGS= -o
8
+#CC= gcc -g -O3
21
 NFLAGS= -o
9
 #CC=gcc -Wall -pedantic -ansi -g -O
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
@@ -35,10 +35,10 @@
22
 
22
 
23
-#for DEC Unix V4.0 
23
 # for Linux
24
 THR_SUBS = pthr_subs
24
 THR_SUBS = pthr_subs2
25
-THR_LIBS = -threads
25
-THR_LIBS = -lpthread
26
+THR_LIBS = -pthread
26
+#THR_LIBS = -lpthread
27
 THR_CC =
27
 THR_CC =
28
 
28
 
29
+#for DEC Unix V4.0 
29
-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
30
+XDIR = ${PREFIX}/bin
43
 
31
 
44
 # renamed (fasta33)  programs
32
 DROPNFA_O = drop_nfa.o
45
-include Makefile33.common
33
 DROPGSW_O = dropgsw.o
46
+#include Makefile33.common
47
 # conventional (fasta3) names
48
-#include Makefile.common
49
+include Makefile.common
(-)fasta3/files/patch-Makefile.common (-20 lines)
Lines 1-20 Link Here
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)
(-)fasta3/files/patch-comp_thr.c (-11 lines)
Lines 1-11 Link Here
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>
(-)fasta3/files/patch-compacc.c (-11 lines)
Lines 1-11 Link Here
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>
(-)fasta3/files/patch-complib.c (-11 lines)
Lines 1-11 Link Here
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>
(-)fasta3/files/patch-scaleswn.c (-11 lines)
Lines 1-11 Link Here
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 */
(-)fasta3/files/pkg-message.in (+16 lines)
Line 0 Link Here
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
==============================================================================
(-)fasta3/pkg-message (-15 lines)
Lines 1-15 Link Here
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
--------------------------------------------------------------------------
(-)fasta3/pkg-plist (-30 / +87 lines)
Lines 1-11 Link Here
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%%

Return to bug 93052