Date: Mon, 29 Jan 2001 16:08:37 +0200 From: johann@egenetics.com To: FreeBSD-gnats-submit@freebsd.org Subject: ports/24716: New port: biology/fasta3 Message-ID: <E14NEyz-0006ef-00@fling.sanbi.ac.za>
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>Number: 24716 >Category: ports >Synopsis: New port: biology/fasta3 >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 06:10:13 PST 2001 >Closed-Date: >Last-Modified: >Originator: Johann Visagie >Release: FreeBSD 5.0-CURRENT i386 >Organization: Electric Genetics >Environment: >Description: - 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) - 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: # # fasta3 # fasta3/Makefile # fasta3/pkg-comment # fasta3/pkg-descr # fasta3/distinfo # fasta3/files # fasta3/files/patch-Makefile # fasta3/files/patch-Makefile.common # fasta3/pkg-plist # fasta3/pkg-message # echo c - fasta3 mkdir -p fasta3 > /dev/null 2>&1 echo x - fasta3/Makefile sed 's/^X//' >fasta3/Makefile << 'END-of-fasta3/Makefile' X# New ports collection makefile for: fasta3 X# Date created: 29 January 2001 X# Whom: Johann Visagie <johann@egenetics.com> X# X# $FreeBSD$ X# X XPORTNAME= fasta3 XPORTVERSION= 33.t08 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}/fasta3 XPKGMESSAGE= ${WRKDIR}/pkg-message XFASTA3_DOCDIR= ${PREFIX}/share/doc/fasta3 XFASTA3_DOCS= 00README.1st README COPYRIGHT fasta3x.me fasta3x.doc \ X readme.* X XMAN1= fasta3.1 fastf3.1 fasts3.1 map_db.1 prss3.1 XMLINKS= fasta3.1 tfasta3.1 fasta3.1 fastx3.1 fasta3.1 tfastx3.1 \ X fasta3.1 fasty3.1 fasta3.1 tfasty3.1 fasta3.1 ssearch3.1 \ X fastf3.1 tfastf3.1 fasts3.1 tfasts3.1 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 @ ${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample X.for manpage in ${MAN1} X @ ${INSTALL_MAN} ${WRKSRC}/${manpage} ${MAN1PREFIX}/man/man1/ X.endfor X.if !defined(NOPORTDOCS) X @ ${MKDIR} ${FASTA3_DOCDIR} X.for docfile in ${FASTA3_DOCS} X @ ${INSTALL_MAN} ${WRKSRC}/${docfile} ${FASTA3_DOCDIR} X.endfor X.endif X.if !defined(BATCH) X @ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' pkg-message > ${PKGMESSAGE} X @ ${CAT} ${PKGMESSAGE} X.endif X X.include <bsd.port.mk> END-of-fasta3/Makefile echo x - fasta3/pkg-comment sed 's/^X//' >fasta3/pkg-comment << 'END-of-fasta3/pkg-comment' XA collection of programs for searching DNA and protein databases, version 3 END-of-fasta3/pkg-comment echo x - fasta3/pkg-descr sed 's/^X//' >fasta3/pkg-descr << 'END-of-fasta3/pkg-descr' XVersion 3 of the FASTA packages contains many programs for searching DNA and Xprotein databases and one program (prss3) for evaluating statistical Xsignificance from randomly shuffled sequences. Several additional analysis Xprograms, including programs that produce local alignments, are available as Xpart of version 2 of the FASTA package, which is available as the port Xbiology/fasta. X XFASTA is described in: W. R. Pearson and D. J. Lipman (1988), "Improved XTools for Biological Sequence Analysis", PNAS 85:2444-2448; W. R. Pearson X(1996) "Effective protein sequence comparison" Meth. Enzymol. 266:227-258; XPearson et. al. (1997) Genomics 46:24-36; Pearson, (1999) Meth. in XMolecular Biology 132:185-219. X XThe FASTA3 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-fasta3/pkg-descr echo x - fasta3/distinfo sed 's/^X//' >fasta3/distinfo << 'END-of-fasta3/distinfo' XMD5 (fasta33t08.shar.Z) = 94f702aa1e9e25c44806088ff6871409 END-of-fasta3/distinfo echo c - fasta3/files mkdir -p fasta3/files > /dev/null 2>&1 echo x - fasta3/files/patch-Makefile sed 's/^X//' >fasta3/files/patch-Makefile << 'END-of-fasta3/files/patch-Makefile' X--- Makefile.orig Mon Jan 29 13:44:28 2001 X+++ Makefile Mon Jan 29 14:08:43 2001 X@@ -12,13 +12,13 @@ X X # use -DBIG_LIB64 to generate 64-bit offsets in map_db .xin files X X-CC= cc -O -std1 X+#CC= cc -O -std1 X #CC= insure -g -DDEBUG X #CC= cc -g -DDEBUG -std1 X #CC= gcc -g -Wall X # X # standard line for normal searching X-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 X+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 X # -I/usr/local/include/mysql -DMYSQL_DB X #(for mySQL databases) (also requires change to Makefile33.common) X X@@ -32,11 +32,15 @@ X HFLAGS= -o X NFLAGS= -o X X-#for DEC Unix V4.0 X THR_SUBS = pthr_subs X-THR_LIBS = -threads X+THR_LIBS = -pthread X THR_CC = X X+#for DEC Unix V4.0 X+#THR_SUBS = pthr_subs X+#THR_LIBS = -threads X+#THR_CC = X+ X #for Sun X #THR_SUBS = uthr_subs X #THR_LIBS = -lthread X@@ -53,9 +57,9 @@ X #THR_LIBS = -lpthreads X #THR_CC = X X-XDIR = /seqprg/slib/bin X+XDIR = ${PREFIX}/bin X X # renamed (fasta33) programs X-include Makefile33.common X+# include Makefile33.common X # conventional (fasta3) names X-#include Makefile.common X+include Makefile.common END-of-fasta3/files/patch-Makefile echo x - fasta3/files/patch-Makefile.common sed 's/^X//' >fasta3/files/patch-Makefile.common << 'END-of-fasta3/files/patch-Makefile.common' X--- Makefile.common.orig Mon Jan 29 12:42:32 2001 X+++ Makefile.common Mon Jan 29 13:44:06 2001 X@@ -46,7 +46,7 @@ X XTPROGS = fastx33_t tfastx33_t fasty33_t tfasty33_t X XPROGS = fastx33 tfastx33 fasty33 tfasty33 X X-PROGS = $(SPROGS) $(TPROGS) X+PROGS = $(SPROGS) $(TPROGS) $(APROGS) $(XTPROGS) $(XPROGS) X X all : $(PROGS) X X@@ -60,7 +60,7 @@ X rm -f *.o $(PROGS) X X install: X- cp $(PROGS) $(XDIR) X+ $(BSD_INSTALL_PROGRAM) $(PROGS) $(XDIR) X X sinstall: X cp $(SPROGS) $(XDIR) END-of-fasta3/files/patch-Makefile.common echo x - fasta3/pkg-plist sed 's/^X//' >fasta3/pkg-plist << 'END-of-fasta3/pkg-plist' X%%PORTDOCS%%share/doc/fasta3/00README.1st X%%PORTDOCS%%share/doc/fasta3/COPYRIGHT X%%PORTDOCS%%share/doc/fasta3/README X%%PORTDOCS%%share/doc/fasta3/fasta3x.doc X%%PORTDOCS%%share/doc/fasta3/fasta3x.me X%%PORTDOCS%%share/doc/fasta3/readme.mpi_3.3 X%%PORTDOCS%%share/doc/fasta3/readme.pvm_2.0 X%%PORTDOCS%%share/doc/fasta3/readme.pvm_3.0 X%%PORTDOCS%%share/doc/fasta3/readme.pvm_3.2 X%%PORTDOCS%%share/doc/fasta3/readme.pvm_3.3 X%%PORTDOCS%%share/doc/fasta3/readme.pvm_3.4 X%%PORTDOCS%%share/doc/fasta3/readme.v30 X%%PORTDOCS%%share/doc/fasta3/readme.v30t6 X%%PORTDOCS%%share/doc/fasta3/readme.v30t7 X%%PORTDOCS%%share/doc/fasta3/readme.v31t0 X%%PORTDOCS%%share/doc/fasta3/readme.v31t1 X%%PORTDOCS%%share/doc/fasta3/readme.v32t0 X%%PORTDOCS%%share/doc/fasta3/readme.v33t0 X%%PORTDOCS%%share/doc/fasta3/readme.w32 Xbin/fasta3 Xbin/fasta3_t Xbin/fastf3 Xbin/fastf3_t Xbin/fasts3 Xbin/fasts3_t Xbin/fastx3 Xbin/fastx3_t Xbin/fasty3 Xbin/fasty3_t Xbin/map_db Xbin/prss3 Xbin/ssearch3 Xbin/ssearch3_t Xbin/tfasta3 Xbin/tfasta3_t Xbin/tfastf3 Xbin/tfastf3_t Xbin/tfasts3 Xbin/tfasts3_t Xbin/tfastx3 Xbin/tfastx3_t Xbin/tfasty3 Xbin/tfasty3_t Xetc/fastlibs.sample X%%PORTDOCS%%@dirrm share/doc/fasta3 END-of-fasta3/pkg-plist echo x - fasta3/pkg-message sed 's/^X//' >fasta3/pkg-message << 'END-of-fasta3/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-fasta3/pkg-message 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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