Date: Mon, 14 Jan 2002 12:35:44 +1100 (EST) From: Camson Huynh <chuynh@biolateral.com.au> To: FreeBSD-gnats-submit@freebsd.org Subject: ports/33853: New Port: biology/tRNAscan-SE Message-ID: <200201140135.g0E1Zif01259@gateway.biolateral.com.au>
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>Number: 33853 >Category: ports >Synopsis: New Port: biology/tRNAscan-SE >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: Sun Jan 13 17:40:01 PST 2002 >Closed-Date: >Last-Modified: >Originator: Camson Huynh >Release: FreeBSD 4.5-PRERELEASE i386 >Organization: BioLateral Pty Ltd >Environment: System: FreeBSD oasis.bio 4.5-PRERELEASE FreeBSD 4.5-PRERELEASE #2: Mon Dec 24 11:32:35 EST 2001 root@oasis.bio:/usr/obj/usr/src/sys/OASIS i386 >Description: tRNAscan-SE was written in the PERL (version 5.0) script language. Input consists of DNA or RNA sequences in FASTA format. tRNA predictions are output in standard tabular or ACeDB format. tRNAscan-SE does no tRNA detection itself, but instead combines the strengths of three independent tRNA prediction programs by negotiating the flow of information between them, performing a limited amount of post-processing, and outputting the results in one of several formats. WWW: http://www.genetics.wustl.edu/eddy/software/ >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: # # tRNAscan-SE # tRNAscan-SE/files # tRNAscan-SE/files/patch-aa # tRNAscan-SE/pkg-comment # tRNAscan-SE/pkg-plist # tRNAscan-SE/Makefile # tRNAscan-SE/distinfo # tRNAscan-SE/pkg-descr # echo c - tRNAscan-SE mkdir -p tRNAscan-SE > /dev/null 2>&1 echo c - tRNAscan-SE/files mkdir -p tRNAscan-SE/files > /dev/null 2>&1 echo x - tRNAscan-SE/files/patch-aa sed 's/^X//' >tRNAscan-SE/files/patch-aa << 'END-of-tRNAscan-SE/files/patch-aa' X--- Makefile.orig Sat Oct 7 00:16:41 2000 X+++ Makefile Thu Dec 20 17:26:37 2001 X@@ -19,10 +19,11 @@ X ## (this could be 'perl5' or otherwise on some systems) X PERLBIN = perl X X+prefix = ${PREFIX} X ## where you want things installed X-BINDIR = $(HOME)/bin X-LIBDIR = $(HOME)/lib/tRNAscan-SE X-MANDIR = $(HOME)/man X+BINDIR = $(prefix)/bin X+LIBDIR = $(prefix)/share/tRNAscan-SE X+MANDIR = $(prefix)/man X X ## NOTE !! If you later manually move the location of X ## binaries or data files in the BINDIR or LIBDIR directories, X@@ -106,7 +107,7 @@ X X MPOBJ = mpviterbi.o mp-dbviterbi.o X X-all: $(PROGS) tRNAscanSE setpaths X+all: $(PROGS) tRNAscanSE X X covels-SE: $(OBJ) scan_main.o X $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) X@@ -178,7 +179,7 @@ X @echo "" X @rm -f testrun.out X @echo "tRNAscan-SE -d -y -o testrun.out Demo/F22B7.fa" X- @if tRNAscan-SE -d -y -o testrun.out Demo/F22B7.fa; \ X+ @if ./tRNAscan-SE -d -y -o testrun.out Demo/F22B7.fa; \ X then echo ""; \ X else echo "tRNAscan-SE did NOT complete properly."; fi X @if diff testrun.out testrun.ref; \ END-of-tRNAscan-SE/files/patch-aa echo x - tRNAscan-SE/pkg-comment sed 's/^X//' >tRNAscan-SE/pkg-comment << 'END-of-tRNAscan-SE/pkg-comment' XAn improved tool for transfer RNA detection END-of-tRNAscan-SE/pkg-comment echo x - tRNAscan-SE/pkg-plist sed 's/^X//' >tRNAscan-SE/pkg-plist << 'END-of-tRNAscan-SE/pkg-plist' Xbin/tRNAscan-SE Xbin/eufindtRNA Xbin/coves-SE Xbin/covels-SE Xbin/trnascan-1.4 Xshare/tRNAscan-SE/TPCsignal Xshare/tRNAscan-SE/gcode.vertmito Xshare/tRNAscan-SE/gcode.othmito Xshare/tRNAscan-SE/gcode.invmito Xshare/tRNAscan-SE/gcode.echdmito Xshare/tRNAscan-SE/gcode.cilnuc Xshare/tRNAscan-SE/TRNA2ns.cm Xshare/tRNAscan-SE/TRNA2.cm Xshare/tRNAscan-SE/TRNA2-eukns.cm Xshare/tRNAscan-SE/TRNA2-euk.cm Xshare/tRNAscan-SE/TRNA2-bactns.cm Xshare/tRNAscan-SE/TRNA2-bact.cm Xshare/tRNAscan-SE/TRNA2-archns.cm Xshare/tRNAscan-SE/TRNA2-arch.cm Xshare/tRNAscan-SE/PSELC.cm Xshare/tRNAscan-SE/ESELC.cm Xshare/tRNAscan-SE/Dsignal Xshare/tRNAscan-SE/gcode.ystmito X@dirrm share/tRNAscan-SE X%%PORTDOCS%%share/doc/tRNAscan-SE/Manual.ps X%%PORTDOCS%%@dirrm share/doc/tRNAscan-SE END-of-tRNAscan-SE/pkg-plist echo x - tRNAscan-SE/Makefile sed 's/^X//' >tRNAscan-SE/Makefile << 'END-of-tRNAscan-SE/Makefile' X# New ports collection makefile for: tRNAscan-SE X# Date created: 15 Jan 2002 X# Whom: chuynh@biolateral.com.au X# X# $FreeBSD$ X# X XPORTNAME= tRNAscan-SE XPORTVERSION= 1.21 XCATEGORIES= biology XMASTER_SITES= ftp://ftp.genetics.wustl.edu/pub/eddy/software/ XEXTRACT_SUFX= .tar.Z X XMAINTAINER= chuynh@biolateral.com.au X XWRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} X XMAN1= tRNAscan-SE.1 X X# X# have to install before testing as path to data files is hardcoded X# Xpost-install: X @ cd ${WRKSRC} && $(MAKE) testrun X.if !defined(NOPORTDOCS) X @${MKDIR} ${DOCSDIR} X ${INSTALL_DATA} ${WRKSRC}/Manual.ps ${DOCSDIR} X.endif X X.include <bsd.port.mk> END-of-tRNAscan-SE/Makefile echo x - tRNAscan-SE/distinfo sed 's/^X//' >tRNAscan-SE/distinfo << 'END-of-tRNAscan-SE/distinfo' XMD5 (tRNAscan-SE-1.21.tar.Z) = 8bdb481fbfc46836bf28f637eb96d306 END-of-tRNAscan-SE/distinfo echo x - tRNAscan-SE/pkg-descr sed 's/^X//' >tRNAscan-SE/pkg-descr << 'END-of-tRNAscan-SE/pkg-descr' XtRNAscan-SE was written in the PERL (version 5.0) script language. XInput consists of DNA or RNA sequences in FASTA format. tRNA Xpredictions are output in standard tabular or ACeDB format. XtRNAscan-SE does no tRNA detection itself, but instead combines the Xstrengths of three independent tRNA prediction programs by negotiating Xthe flow of information between them, performing a limited amount of Xpost-processing, and outputting the results in one of several Xformats. X XWWW: http://www.genetics.wustl.edu/eddy/software/ END-of-tRNAscan-SE/pkg-descr 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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