- New port: biology/fasta3, which comprises the FASTA3 suite of DNA and

  protein sequence search programs
- FASTA3 updates only some of the elements of FASTA2, which is why I have
  submitted ports of both versions (as biology/fasta and biology/fasta3)

PR:		24716
Submitted by:	Johann Visagie <johann@egenetics.com>

9 files changed, 204 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 0e5e7c5dfae0..880d5e36e467 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -8,6 +8,7 @@
     SUBDIR += deft
     SUBDIR += emboss
     SUBDIR += fasta
+    SUBDIR += fasta3
     SUBDIR += fastdnaml
     SUBDIR += gaussian98
     SUBDIR += gperiodic
diff --git a/biology/fasta3/Makefile b/biology/fasta3/Makefile
new file mode 100644
index 000000000000..c7b27e097cab
--- /dev/null
+++ b/biology/fasta3/Makefile
@@ -0,0 +1,52 @@
+# New ports collection makefile for:	fasta3
+# Date created:		29 January 2001
+# Whom:	      		Johann Visagie <johann@egenetics.com>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	fasta3
+PORTVERSION=	33.t08
+CATEGORIES=	biology
+MASTER_SITES=	http://ftp.virginia.edu/pub/fasta/
+DISTNAME=	fasta${PORTVERSION:S/.//g}
+EXTRACT_SUFX=	.shar.Z
+
+MAINTAINER=	johann@egenetics.com
+
+NO_CDROM=	May not be sold or incorporated into a commercial product
+WRKSRC=		${WRKDIR}/fasta3
+PKGMESSAGE=	${WRKDIR}/pkg-message
+FASTA3_DOCDIR=	${PREFIX}/share/doc/fasta3
+FASTA3_DOCS=	00README.1st README COPYRIGHT fasta3x.me fasta3x.doc \
+		readme.*
+
+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  \
+		fasta3.1 fasty3.1  fasta3.1 tfasty3.1 fasta3.1 ssearch3.1 \
+		fastf3.1 tfastf3.1 fasts3.1 tfasts3.1
+
+do-extract:
+	@ ${RM} -rf ${WRKDIR}
+	@ ${MKDIR} ${WRKSRC}
+	@ for file in ${EXTRACT_ONLY}; do \
+	  cd ${WRKSRC} && (${GZCAT} ${DISTDIR}/$${file} | ${SH} >/dev/null); \
+	done
+
+post-install:
+	@ ${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample
+.for manpage in ${MAN1}
+	@ ${INSTALL_MAN} ${WRKSRC}/${manpage} ${MAN1PREFIX}/man/man1/
+.endfor
+.if !defined(NOPORTDOCS)
+	@ ${MKDIR} ${FASTA3_DOCDIR}
+.for docfile in ${FASTA3_DOCS}
+	@ ${INSTALL_MAN} ${WRKSRC}/${docfile} ${FASTA3_DOCDIR}
+.endfor
+.endif
+.if !defined(BATCH)
+	@ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' pkg-message > ${PKGMESSAGE}
+	@ ${CAT} ${PKGMESSAGE}
+.endif
+
+.include <bsd.port.mk>
diff --git a/biology/fasta3/distinfo b/biology/fasta3/distinfo
new file mode 100644
index 000000000000..d04229bf215c
--- /dev/null
+++ b/biology/fasta3/distinfo
@@ -0,0 +1 @@
+MD5 (fasta33t08.shar.Z) = 94f702aa1e9e25c44806088ff6871409
diff --git a/biology/fasta3/files/patch-Makefile b/biology/fasta3/files/patch-Makefile
new file mode 100644
index 000000000000..bdc135f01c97
--- /dev/null
+++ b/biology/fasta3/files/patch-Makefile
@@ -0,0 +1,49 @@
+--- Makefile.orig	Mon Jan 29 13:44:28 2001
++++ Makefile	Mon Jan 29 14:08:43 2001
+@@ -12,13 +12,13 @@
+ 
+ # 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
++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
+ # -I/usr/local/include/mysql -DMYSQL_DB 
+ #(for mySQL databases)  (also requires change to Makefile33.common)
+ 
+@@ -32,11 +32,15 @@
+ HFLAGS= -o
+ NFLAGS= -o
+ 
+-#for DEC Unix V4.0 
+ THR_SUBS = pthr_subs
+-THR_LIBS = -threads
++THR_LIBS = -pthread
+ THR_CC =
+ 
++#for DEC Unix V4.0 
++#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
+ 
+ # renamed (fasta33)  programs
+-include Makefile33.common
++# include Makefile33.common
+ # conventional (fasta3) names
+-#include Makefile.common
++include Makefile.common
diff --git a/biology/fasta3/files/patch-Makefile.common b/biology/fasta3/files/patch-Makefile.common
new file mode 100644
index 000000000000..395da695e031
--- /dev/null
+++ b/biology/fasta3/files/patch-Makefile.common
@@ -0,0 +1,20 @@
+--- 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)
diff --git a/biology/fasta3/pkg-comment b/biology/fasta3/pkg-comment
new file mode 100644
index 000000000000..42bea2b9a553
--- /dev/null
+++ b/biology/fasta3/pkg-comment
@@ -0,0 +1 @@
+A collection of programs for searching DNA and protein databases, V 3
diff --git a/biology/fasta3/pkg-descr b/biology/fasta3/pkg-descr
new file mode 100644
index 000000000000..9aac7813aa95
--- /dev/null
+++ b/biology/fasta3/pkg-descr
@@ -0,0 +1,20 @@
+Version 3 of the FASTA packages contains many programs for searching DNA and
+protein databases and one program (prss3) for evaluating statistical
+significance from randomly shuffled sequences.  Several additional analysis
+programs, including programs that produce local alignments, are available as
+part of version 2 of the FASTA package, which is available as the port
+biology/fasta.
+
+FASTA is described in:  W. R. Pearson and D. J. Lipman (1988), "Improved
+Tools for Biological Sequence Analysis", PNAS 85:2444-2448; W. R.  Pearson
+(1996) "Effective protein sequence comparison" Meth. Enzymol.  266:227-258;
+Pearson et. al.  (1997) Genomics 46:24-36;  Pearson, (1999) Meth. in
+Molecular Biology 132:185-219.
+
+The FASTA3 suite is distributed freely subject to the condition that it may
+not be sold or incorporated into a commercial product.
+
+Author: William R Pearson <wrp@virginia.edu>
+WWW:    http://fasta.bioch.virginia.edu/
+
+-- Johann Visagie <johann@egenetics.com>
diff --git a/biology/fasta3/pkg-message b/biology/fasta3/pkg-message
new file mode 100644
index 000000000000..4a6cc7e32515
--- /dev/null
+++ b/biology/fasta3/pkg-message
@@ -0,0 +1,15 @@
+--------------------------------------------------------------------------
+
+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"
+
+--------------------------------------------------------------------------
diff --git a/biology/fasta3/pkg-plist b/biology/fasta3/pkg-plist
new file mode 100644
index 000000000000..a73cd6e197a8
--- /dev/null
+++ b/biology/fasta3/pkg-plist
@@ -0,0 +1,45 @@
+%%PORTDOCS%%share/doc/fasta3/00README.1st
+%%PORTDOCS%%share/doc/fasta3/COPYRIGHT
+%%PORTDOCS%%share/doc/fasta3/README
+%%PORTDOCS%%share/doc/fasta3/fasta3x.doc
+%%PORTDOCS%%share/doc/fasta3/fasta3x.me
+%%PORTDOCS%%share/doc/fasta3/readme.mpi_3.3
+%%PORTDOCS%%share/doc/fasta3/readme.pvm_2.0
+%%PORTDOCS%%share/doc/fasta3/readme.pvm_3.0
+%%PORTDOCS%%share/doc/fasta3/readme.pvm_3.2
+%%PORTDOCS%%share/doc/fasta3/readme.pvm_3.3
+%%PORTDOCS%%share/doc/fasta3/readme.pvm_3.4
+%%PORTDOCS%%share/doc/fasta3/readme.v30
+%%PORTDOCS%%share/doc/fasta3/readme.v30t6
+%%PORTDOCS%%share/doc/fasta3/readme.v30t7
+%%PORTDOCS%%share/doc/fasta3/readme.v31t0
+%%PORTDOCS%%share/doc/fasta3/readme.v31t1
+%%PORTDOCS%%share/doc/fasta3/readme.v32t0
+%%PORTDOCS%%share/doc/fasta3/readme.v33t0
+%%PORTDOCS%%share/doc/fasta3/readme.w32
+bin/fasta3
+bin/fasta3_t
+bin/fastf3
+bin/fastf3_t
+bin/fasts3
+bin/fasts3_t
+bin/fastx3
+bin/fastx3_t
+bin/fasty3
+bin/fasty3_t
+bin/map_db
+bin/prss3
+bin/ssearch3
+bin/ssearch3_t
+bin/tfasta3
+bin/tfasta3_t
+bin/tfastf3
+bin/tfastf3_t
+bin/tfasts3
+bin/tfasts3_t
+bin/tfastx3
+bin/tfastx3_t
+bin/tfasty3
+bin/tfasty3_t
+etc/fastlibs.sample
+%%PORTDOCS%%@dirrm share/doc/fasta3