Date: Mon, 29 Jan 2001 16:06:29 +0200 From: johann@egenetics.com To: FreeBSD-gnats-submit@freebsd.org Subject: ports/24715: New port: biology/fasta Message-ID: <E14NEwv-0006cg-00@fling.sanbi.ac.za>
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>Number: 24715 >Category: ports >Synopsis: New port: biology/fasta >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Mon Jan 29 06:10:11 PST 2001 >Closed-Date: >Last-Modified: >Originator: Johann Visagie >Release: FreeBSD 5.0-CURRENT i386 >Organization: Electric Genetics >Environment: >Description: - New port: biology/fasta, the FASTA2 suite of DNA and protein sequence search tools - FASTA2 is only maintained for bugfixes, but still includes some programs which are not in FASTA3 (of which I'll submit a port right after this) - Only tested on -CURRENT >How-To-Repeat: >Fix: # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # fasta # fasta/files # fasta/files/patch-Makefile # fasta/pkg-comment # fasta/pkg-descr # fasta/Makefile # fasta/pkg-plist # fasta/pkg-message # fasta/distinfo # echo c - fasta mkdir -p fasta > /dev/null 2>&1 echo c - fasta/files mkdir -p fasta/files > /dev/null 2>&1 echo x - fasta/files/patch-Makefile sed 's/^X//' >fasta/files/patch-Makefile << 'END-of-fasta/files/patch-Makefile' X--- Makefile.orig Mon Jan 29 15:10:42 2001 X+++ Makefile Mon Jan 29 15:15:08 2001 X@@ -3,13 +3,13 @@ X # for mips, also use: -mips2 -O2 X # X X-CC= cc -O X+#CC= cc -O X #CC=cc -g X X-CFLAGS= -DUNIX -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS X+CFLAGS+= -DUNIX -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS X LFLAGS= -lm -o X X-BIN = /seqprg/slib/bin X+BIN = $(PREFIX)/bin X #NRAND= nrand X #IBM RS/6000 X NRAND= nrand48 X@@ -29,7 +29,7 @@ X sall : $(SPROGS) X X install : X- cp $(PROGS) $(BIN) X+ $(BSD_INSTALL_PROGRAM) $(PROGS) $(BIN) X X clean-up : X rm *.o $(PROGS) END-of-fasta/files/patch-Makefile echo x - fasta/pkg-comment sed 's/^X//' >fasta/pkg-comment << 'END-of-fasta/pkg-comment' XA collection of programs for searching DNA and protein databases END-of-fasta/pkg-comment echo x - fasta/pkg-descr sed 's/^X//' >fasta/pkg-descr << 'END-of-fasta/pkg-descr' XVersion 2 of the FASTA packages contains many programs for searching DNA and Xprotein databases, performing sequence comparisons, producing local Xalignments, and other related tasks. X XCurrently, the FASTA2 suite is in maintenance mode. Updated versions of ONLY Xthe searching programs are available in version 3 of the FASTA packages, Xwhich may be found in the port biology/fasta3. X XFASTA is described in: W. R. Pearson and D. J. Lipman (1988), "Improved XTools for Biological Sequence Analysis", PNAS 85:2444- 2448, and W. R. XPearson (1990) "Rapid and Sensitive Sequence Comparison with FASTP and FASTA" XMethods in Enzymology 183:63- 98). X XThe FASTA2 suite is distributed freely subject to the condition that it may Xnot be sold or incorporated into a commercial product. X XAuthor: William R Pearson <wrp@virginia.edu> XWWW: http://fasta.bioch.virginia.edu/ X X-- Johann Visagie <johann@egenetics.com> END-of-fasta/pkg-descr echo x - fasta/Makefile sed 's/^X//' >fasta/Makefile << 'END-of-fasta/Makefile' X# New ports collection makefile for: fasta X# Date created: 29 January 2001 X# Whom: Johann Visagie <johann@egenetics.com> X# X# $FreeBSD$ X# X XPORTNAME= fasta XPORTVERSION= 20.u66 XCATEGORIES= biology XMASTER_SITES= http://ftp.virginia.edu/pub/fasta/ XDISTNAME= fasta${PORTVERSION:S/.//g} XEXTRACT_SUFX= .shar.Z X XMAINTAINER= johann@egenetics.com X XNO_CDROM= May not be sold or incorporated into a commercial product XWRKSRC= ${WRKDIR}/fasta XPKGMESSAGE= ${WRKDIR}/pkg-message XFASTA_DOCDIR= ${PREFIX}/share/doc/fasta XFASTA_DOCS= COPYRIGHT README.versions fasta20.doc fasta20.me format.doc \ X readme.* X XMAN1= align.1 fasta.1 lalign.1 prdf.1 prss.1 randseq.1 ssearch.1 XMLINKS= fasta.1 tfasta.1 fasta.1 lfasta.1 fasta.1 plfasta.1 \ X fasta.1 fastx.1 fasta.1 tfastx.1 \ X align.1 align0.1 lalign.1 plalign.1 X Xdo-extract: X @ ${RM} -rf ${WRKDIR} X @ ${MKDIR} ${WRKSRC} X @ for file in ${EXTRACT_ONLY}; do \ X cd ${WRKSRC} && (${GZCAT} ${DISTDIR}/$${file} | ${SH} >/dev/null); \ X done X Xpost-install: X.for manpage in ${MAN1} X @ ${INSTALL_MAN} ${WRKSRC}/${manpage} ${MAN1PREFIX}/man/man1/ X.endfor X.if !defined(NOPORTDOCS) X @ ${MKDIR} ${FASTA_DOCDIR} X.for docfile in ${FASTA_DOCS} X @ ${INSTALL_MAN} ${WRKSRC}/${docfile} ${FASTA_DOCDIR} X.endfor X.endif X X.include <bsd.port.mk> END-of-fasta/Makefile echo x - fasta/pkg-plist sed 's/^X//' >fasta/pkg-plist << 'END-of-fasta/pkg-plist' X%%PORTDOCS%%share/doc/fasta/COPYRIGHT X%%PORTDOCS%%share/doc/fasta/README.versions X%%PORTDOCS%%share/doc/fasta/fasta20.doc X%%PORTDOCS%%share/doc/fasta/fasta20.me X%%PORTDOCS%%share/doc/fasta/format.doc X%%PORTDOCS%%share/doc/fasta/readme.v15 X%%PORTDOCS%%share/doc/fasta/readme.v16 X%%PORTDOCS%%share/doc/fasta/readme.v17 X%%PORTDOCS%%share/doc/fasta/readme.v20 X%%PORTDOCS%%share/doc/fasta/readme.v20u4 X%%PORTDOCS%%share/doc/fasta/readme.v20u5 X%%PORTDOCS%%share/doc/fasta/readme.v20u6 Xbin/aacomp Xbin/align Xbin/align0 Xbin/bestscor Xbin/crandseq Xbin/fasta Xbin/fastx Xbin/flalign Xbin/fromgb Xbin/garnier Xbin/grease Xbin/lalign Xbin/lfasta Xbin/plalign Xbin/plfasta Xbin/prdf Xbin/prss Xbin/psgrease Xbin/randseq Xbin/relate Xbin/ssearch Xbin/tfasta Xbin/tfastx Xbin/tgrease Xbin/zs_exp X%%PORTDOCS%%@dirrm share/doc/fasta END-of-fasta/pkg-plist echo x - fasta/pkg-message sed 's/^X//' >fasta/pkg-message << 'END-of-fasta/pkg-message' X-------------------------------------------------------------------------- X XThe FASTA3 package has been successfully installed. X XNB: A sample configuration file has been installed to %%PREFIX%%/etc as X"fastlibs.sample". This may be renamed to "fastlibs" and edited Xto suit the requirements of a particular site. X XIn order to use the FASTA3 programs, a user must set the environment Xvariable FASTLIBS to contain the full path of the FASTA3 configuration Xfile, e.g.: X X- set FASTLIBS to: "%%PREFIX%%/etc/fastlibs" X X-------------------------------------------------------------------------- END-of-fasta/pkg-message echo x - fasta/distinfo sed 's/^X//' >fasta/distinfo << 'END-of-fasta/distinfo' XMD5 (fasta20u66.shar.Z) = 3960df040e5006969cf02568544751e9 END-of-fasta/distinfo exit >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
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