Attachment 87278 Details for Bug 123866 – file.diff

[patch] file.diff

file.diff (text/plain), 4.73 KB, created by tkato432 on 2008-05-21 18:10:01 UTC

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Creator: tkato432

Created: 2008-05-21 18:10:01 UTC

Size: 4.73 KB

patch

obsolete

>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%%

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Attachments on bug 123866: 87278