From c82fc943113baf5de2e9b2282c7f015ba8965de9 Mon Sep 17 00:00:00 2001 From: "James E. Housley" Date: Sun, 11 Feb 2001 16:24:18 +0000 Subject: New port: biology/fasta, the FASTA2 suite of DNA and protein sequence search tools PR: 24715 Submitted by: Johann Visagie --- biology/fasta/Makefile | 47 ++++++++++++++++++++++++++++++++++++++ biology/fasta/distinfo | 1 + biology/fasta/files/patch-Makefile | 28 +++++++++++++++++++++++ biology/fasta/pkg-comment | 1 + biology/fasta/pkg-descr | 20 ++++++++++++++++ biology/fasta/pkg-message | 15 ++++++++++++ biology/fasta/pkg-plist | 38 ++++++++++++++++++++++++++++++ 7 files changed, 150 insertions(+) create mode 100644 biology/fasta/Makefile create mode 100644 biology/fasta/distinfo create mode 100644 biology/fasta/files/patch-Makefile create mode 100644 biology/fasta/pkg-comment create mode 100644 biology/fasta/pkg-descr create mode 100644 biology/fasta/pkg-message create mode 100644 biology/fasta/pkg-plist (limited to 'biology/fasta') diff --git a/biology/fasta/Makefile b/biology/fasta/Makefile new file mode 100644 index 000000000000..a5cff36068c4 --- /dev/null +++ b/biology/fasta/Makefile @@ -0,0 +1,47 @@ +# New ports collection makefile for: fasta +# Date created: 29 January 2001 +# Whom: Johann Visagie +# +# $FreeBSD$ +# + +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 diff --git a/biology/fasta/distinfo b/biology/fasta/distinfo new file mode 100644 index 000000000000..d1bcef75803b --- /dev/null +++ b/biology/fasta/distinfo @@ -0,0 +1 @@ +MD5 (fasta20u66.shar.Z) = 3960df040e5006969cf02568544751e9 diff --git a/biology/fasta/files/patch-Makefile b/biology/fasta/files/patch-Makefile new file mode 100644 index 000000000000..25262482eef8 --- /dev/null +++ b/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) diff --git a/biology/fasta/pkg-comment b/biology/fasta/pkg-comment new file mode 100644 index 000000000000..b4e576aaaea1 --- /dev/null +++ b/biology/fasta/pkg-comment @@ -0,0 +1 @@ +A collection of programs for searching DNA and protein databases diff --git a/biology/fasta/pkg-descr b/biology/fasta/pkg-descr new file mode 100644 index 000000000000..b5230be12f67 --- /dev/null +++ b/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 +WWW: http://fasta.bioch.virginia.edu/ + +-- Johann Visagie diff --git a/biology/fasta/pkg-message b/biology/fasta/pkg-message new file mode 100644 index 000000000000..4a6cc7e32515 --- /dev/null +++ b/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" + +-------------------------------------------------------------------------- diff --git a/biology/fasta/pkg-plist b/biology/fasta/pkg-plist new file mode 100644 index 000000000000..7b65ef9c827a --- /dev/null +++ b/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 -- cgit v1.2.3