New port: biology/fasta, the FASTA2 suite of DNA and protein sequence

search tools

PR:		24715
Submitted by:	Johann Visagie <johann@egenetics.com>

biology/Makefile

@@ -7,6 +7,7 @@
     SUBDIR += clustalw
     SUBDIR += deft
     SUBDIR += emboss
+    SUBDIR += fasta
     SUBDIR += fastdnaml
     SUBDIR += gaussian98
     SUBDIR += gperiodic

biology/fasta/Makefile

@@ -0,0 +1,47 @@
+# New ports collection makefile for:	fasta
+# Date created:		29 January 2001
+# Whom:	      		Johann Visagie <johann@egenetics.com>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	fasta
+PORTVERSION=	20.u66
+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}/fasta
+PKGMESSAGE=	${WRKDIR}/pkg-message
+FASTA_DOCDIR=	${PREFIX}/share/doc/fasta
+FASTA_DOCS=	COPYRIGHT README.versions fasta20.doc fasta20.me format.doc \
+		readme.*
+
+MAN1=		align.1 fasta.1 lalign.1 prdf.1 prss.1 randseq.1 ssearch.1
+MLINKS=		fasta.1 tfasta.1 fasta.1 lfasta.1 fasta.1 plfasta.1 \
+		fasta.1 fastx.1  fasta.1 tfastx.1 \
+		align.1 align0.1 lalign.1 plalign.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:
+.for manpage in ${MAN1}
+	@ ${INSTALL_MAN} ${WRKSRC}/${manpage} ${MAN1PREFIX}/man/man1/
+.endfor
+.if !defined(NOPORTDOCS)
+	@ ${MKDIR} ${FASTA_DOCDIR}
+.for docfile in ${FASTA_DOCS}
+	@ ${INSTALL_MAN} ${WRKSRC}/${docfile} ${FASTA_DOCDIR}
+.endfor
+.endif
+
+.include <bsd.port.mk>

biology/fasta/distinfo

@@ -0,0 +1 @@
+MD5 (fasta20u66.shar.Z) = 3960df040e5006969cf02568544751e9

biology/fasta/files/patch-Makefile

@@ -0,0 +1,28 @@
+--- Makefile.orig	Mon Jan 29 15:10:42 2001
++++ Makefile	Mon Jan 29 15:15:08 2001
+@@ -3,13 +3,13 @@
+ # for mips, also use: -mips2 -O2
+ #
+ 
+-CC= cc -O
++#CC= cc -O
+ #CC=cc -g
+ 
+-CFLAGS= -DUNIX -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS
++CFLAGS+= -DUNIX -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS
+ LFLAGS= -lm -o
+ 
+-BIN = /seqprg/slib/bin
++BIN = $(PREFIX)/bin
+ #NRAND= nrand
+ #IBM RS/6000
+ NRAND= nrand48
+@@ -29,7 +29,7 @@
+ sall : $(SPROGS)
+ 
+ install : 
+-	cp $(PROGS) $(BIN)
++	$(BSD_INSTALL_PROGRAM) $(PROGS) $(BIN)
+ 
+ clean-up : 
+ 	rm *.o $(PROGS)

biology/fasta/pkg-comment

@@ -0,0 +1 @@
+A collection of programs for searching DNA and protein databases

biology/fasta/pkg-descr

@@ -0,0 +1,20 @@
+Version 2 of the FASTA packages contains many programs for searching DNA and
+protein databases, performing sequence comparisons, producing local
+alignments, and other related tasks.
+
+Currently, the FASTA2 suite is in maintenance mode.  Updated versions of ONLY
+the searching programs are available in version 3 of the FASTA packages,
+which may be found in the port biology/fasta3.
+
+FASTA is described in:  W. R. Pearson and D. J. Lipman (1988), "Improved
+Tools for Biological Sequence Analysis", PNAS 85:2444- 2448, and W. R.
+Pearson (1990) "Rapid and Sensitive Sequence Comparison with FASTP and FASTA"
+Methods in Enzymology 183:63- 98).
+
+The FASTA2 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>

biology/fasta/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"
+
+--------------------------------------------------------------------------

biology/fasta/pkg-plist

@@ -0,0 +1,38 @@
+%%PORTDOCS%%share/doc/fasta/COPYRIGHT
+%%PORTDOCS%%share/doc/fasta/README.versions
+%%PORTDOCS%%share/doc/fasta/fasta20.doc
+%%PORTDOCS%%share/doc/fasta/fasta20.me
+%%PORTDOCS%%share/doc/fasta/format.doc
+%%PORTDOCS%%share/doc/fasta/readme.v15
+%%PORTDOCS%%share/doc/fasta/readme.v16
+%%PORTDOCS%%share/doc/fasta/readme.v17
+%%PORTDOCS%%share/doc/fasta/readme.v20
+%%PORTDOCS%%share/doc/fasta/readme.v20u4
+%%PORTDOCS%%share/doc/fasta/readme.v20u5
+%%PORTDOCS%%share/doc/fasta/readme.v20u6
+bin/aacomp
+bin/align
+bin/align0
+bin/bestscor
+bin/crandseq
+bin/fasta
+bin/fastx
+bin/flalign
+bin/fromgb
+bin/garnier
+bin/grease
+bin/lalign
+bin/lfasta
+bin/plalign
+bin/plfasta
+bin/prdf
+bin/prss
+bin/psgrease
+bin/randseq
+bin/relate
+bin/ssearch
+bin/tfasta
+bin/tfastx
+bin/tgrease
+bin/zs_exp
+%%PORTDOCS%%@dirrm share/doc/fasta