4 files changed, 46 insertions, 61 deletions

diff --git a/biology/tRNAscan-SE/Makefile b/biology/tRNAscan-SE/Makefile
index 1ffeebff9282..da7e62619150 100644
--- a/biology/tRNAscan-SE/Makefile
+++ b/biology/tRNAscan-SE/Makefile
@@ -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 --git a/biology/tRNAscan-SE/files/patch-aa b/biology/tRNAscan-SE/files/patch-aa
deleted file mode 100644
index 82f9a3b420a0..000000000000
--- a/biology/tRNAscan-SE/files/patch-aa
+++ /dev/null
@@ -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 --git a/biology/tRNAscan-SE/pkg-descr b/biology/tRNAscan-SE/pkg-descr
index 008e02d08a16..288f622a4c1c 100644
--- a/biology/tRNAscan-SE/pkg-descr
+++ b/biology/tRNAscan-SE/pkg-descr
@@ -7,4 +7,4 @@ 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/
+WWW: http://selab.janelia.org/software.html
diff --git a/biology/tRNAscan-SE/pkg-plist b/biology/tRNAscan-SE/pkg-plist
index 3ebf814cc5c0..086d2cf6325b 100644
--- a/biology/tRNAscan-SE/pkg-plist
+++ b/biology/tRNAscan-SE/pkg-plist
@@ -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%%