Date: Thu, 22 May 2008 02:00:10 +0900 From: KATO Tsuguru <tkato432@yahoo.com> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/123866: Update port: biology/tRNAscan-SE Message-ID: <20080522020010.c3749da3.tkato432@yahoo.com> Resent-Message-ID: <200805211710.m4LHA1OT053643@freefall.freebsd.org>
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>Number: 123866 >Category: ports >Synopsis: Update port: biology/tRNAscan-SE >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Wed May 21 17:10:01 UTC 2008 >Closed-Date: >Last-Modified: >Originator: KATO Tsuguru >Release: FreeBSD 6.3-RELEASE-p2 i386 >Organization: >Environment: >Description: - Update MASTER_SITES and WWW: line - Support CC/CFLAGS properly - Strip binary Remove file: files/patch-aa >How-To-Repeat: >Fix: diff -urN /usr/ports/biology/tRNAscan-SE/Makefile biology/tRNAscan-SE/Makefile --- /usr/ports/biology/tRNAscan-SE/Makefile 2008-05-15 15:22:13.000000000 +0900 +++ biology/tRNAscan-SE/Makefile 2008-05-15 15:26:10.000000000 +0900 @@ -7,22 +7,42 @@ PORTNAME= tRNAscan-SE PORTVERSION= 1.23 +PORTREVISION= 1 CATEGORIES= biology -MASTER_SITES= ftp://ftp.genetics.wustl.edu/pub/eddy/software/ +MASTER_SITES= ftp://selab.janelia.org/pub/software/tRNAscan-SE/ EXTRACT_SUFX= .tar.Z MAINTAINER= ports@FreeBSD.org COMMENT= An improved tool for transfer RNA detection +USE_PERL5= yes +MAKE_ARGS= BINDIR="${PREFIX}/bin" \ + LIBDIR="${DATADIR}" \ + CC="${CC}" \ + CFLAGS="${CFLAGS}" + MAN1= tRNAscan-SE.1 -USE_PERL5= yes +post-patch: + @${REINPLACE_CMD} -e 's|tRNAscanSE setpaths|tRNAscanSE|g ; \ + s|if tRNAscan-SE|if ./tRNAscan-SE|g' ${WRKSRC}/Makefile + +do-install: +.for f in covels-SE coves-SE eufindtRNA trnascan-1.4 + ${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin +.endfor + ${INSTALL_SCRIPT} ${WRKSRC}/tRNAscan-SE ${PREFIX}/bin + ${INSTALL_MAN} ${WRKSRC}/tRNAscan-SE.man ${MANPREFIX}/man/man1/tRNAscan-SE.1 + @${MKDIR} ${DATADIR} +.for f in TPCsignal Dsignal *.cm gcode.* + ${INSTALL_DATA} ${WRKSRC}/${f} ${DATADIR} +.endfor # # have to install before testing as path to data files is hardcoded # post-install: - @ cd ${WRKSRC} && $(MAKE) testrun + @ cd ${WRKSRC} && $(MAKE) testrun .if !defined(NOPORTDOCS) @${MKDIR} ${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/Manual.ps ${DOCSDIR} diff -urN /usr/ports/biology/tRNAscan-SE/files/patch-aa biology/tRNAscan-SE/files/patch-aa --- /usr/ports/biology/tRNAscan-SE/files/patch-aa 2002-03-27 23:18:49.000000000 +0900 +++ biology/tRNAscan-SE/files/patch-aa 1970-01-01 09:00:00.000000000 +0900 @@ -1,35 +0,0 @@ ---- Makefile.orig Sat Oct 7 00:16:41 2000 -+++ Makefile Thu Dec 20 17:26:37 2001 -@@ -19,10 +19,11 @@ - ## (this could be 'perl5' or otherwise on some systems) - PERLBIN = perl - -+prefix = ${PREFIX} - ## where you want things installed --BINDIR = $(HOME)/bin --LIBDIR = $(HOME)/lib/tRNAscan-SE --MANDIR = $(HOME)/man -+BINDIR = $(prefix)/bin -+LIBDIR = $(prefix)/share/tRNAscan-SE -+MANDIR = $(prefix)/man - - ## NOTE !! If you later manually move the location of - ## binaries or data files in the BINDIR or LIBDIR directories, -@@ -106,7 +107,7 @@ - - MPOBJ = mpviterbi.o mp-dbviterbi.o - --all: $(PROGS) tRNAscanSE setpaths -+all: $(PROGS) tRNAscanSE - - covels-SE: $(OBJ) scan_main.o - $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) -@@ -178,7 +179,7 @@ - @echo "" - @rm -f testrun.out - @echo "tRNAscan-SE -d -y -o testrun.out Demo/F22B7.fa" -- @if tRNAscan-SE -d -y -o testrun.out Demo/F22B7.fa; \ -+ @if ./tRNAscan-SE -d -y -o testrun.out Demo/F22B7.fa; \ - then echo ""; \ - else echo "tRNAscan-SE did NOT complete properly."; fi - @if diff testrun.out testrun.ref; \ diff -urN /usr/ports/biology/tRNAscan-SE/pkg-descr biology/tRNAscan-SE/pkg-descr --- /usr/ports/biology/tRNAscan-SE/pkg-descr 2002-03-27 23:18:47.000000000 +0900 +++ biology/tRNAscan-SE/pkg-descr 2008-05-13 03:52:57.000000000 +0900 @@ -7,4 +7,4 @@ post-processing, and outputting the results in one of several formats. -WWW: http://www.genetics.wustl.edu/eddy/software/ +WWW: http://selab.janelia.org/software.html diff -urN /usr/ports/biology/tRNAscan-SE/pkg-plist biology/tRNAscan-SE/pkg-plist --- /usr/ports/biology/tRNAscan-SE/pkg-plist 2003-10-22 18:29:53.000000000 +0900 +++ biology/tRNAscan-SE/pkg-plist 2008-05-13 03:17:54.000000000 +0900 @@ -1,26 +1,26 @@ -bin/tRNAscan-SE -bin/eufindtRNA -bin/coves-SE bin/covels-SE +bin/coves-SE +bin/eufindtRNA +bin/tRNAscan-SE bin/trnascan-1.4 -share/tRNAscan-SE/TPCsignal -share/tRNAscan-SE/gcode.vertmito -share/tRNAscan-SE/gcode.othmito -share/tRNAscan-SE/gcode.invmito -share/tRNAscan-SE/gcode.echdmito -share/tRNAscan-SE/gcode.cilnuc -share/tRNAscan-SE/TRNA2ns.cm -share/tRNAscan-SE/TRNA2.cm -share/tRNAscan-SE/TRNA2-eukns.cm -share/tRNAscan-SE/TRNA2-euk.cm -share/tRNAscan-SE/TRNA2-bactns.cm -share/tRNAscan-SE/TRNA2-bact.cm -share/tRNAscan-SE/TRNA2-archns.cm -share/tRNAscan-SE/TRNA2-arch.cm -share/tRNAscan-SE/PSELC.cm -share/tRNAscan-SE/ESELC.cm -share/tRNAscan-SE/Dsignal -share/tRNAscan-SE/gcode.ystmito -@dirrm share/tRNAscan-SE %%PORTDOCS%%%%DOCSDIR%%/Manual.ps +%%DATADIR%%/TPCsignal +%%DATADIR%%/gcode.vertmito +%%DATADIR%%/gcode.othmito +%%DATADIR%%/gcode.invmito +%%DATADIR%%/gcode.echdmito +%%DATADIR%%/gcode.cilnuc +%%DATADIR%%/TRNA2ns.cm +%%DATADIR%%/TRNA2.cm +%%DATADIR%%/TRNA2-eukns.cm +%%DATADIR%%/TRNA2-euk.cm +%%DATADIR%%/TRNA2-bactns.cm +%%DATADIR%%/TRNA2-bact.cm +%%DATADIR%%/TRNA2-archns.cm +%%DATADIR%%/TRNA2-arch.cm +%%DATADIR%%/PSELC.cm +%%DATADIR%%/ESELC.cm +%%DATADIR%%/Dsignal +%%DATADIR%%/gcode.ystmito +@dirrm %%DATADIR%% %%PORTDOCS%%@dirrm %%DOCSDIR%% >Release-Note: >Audit-Trail: >Unformatted:
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