Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection.

PR:		33853
Submitted by:	chuynh@biolateral.com.au

7 files changed, 102 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index ead96e624098..1de3d9e94a34 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -44,6 +44,7 @@
     SUBDIR += seaview
     SUBDIR += seqio
     SUBDIR += sim4
+    SUBDIR += tRNAscan-SE
     SUBDIR += t_coffee
     SUBDIR += tinker
     SUBDIR += treeviewx
diff --git a/biology/tRNAscan-SE/Makefile b/biology/tRNAscan-SE/Makefile
new file mode 100644
index 000000000000..f175f5f1a357
--- /dev/null
+++ b/biology/tRNAscan-SE/Makefile
@@ -0,0 +1,28 @@
+# New ports collection makefile for:	tRNAscan-SE
+# Date created:				15 Jan 2002
+# Whom:					chuynh@biolateral.com.au
+#
+# $FreeBSD$
+#
+
+PORTNAME=	tRNAscan-SE
+PORTVERSION=	1.21
+CATEGORIES=	biology
+MASTER_SITES=	ftp://ftp.genetics.wustl.edu/pub/eddy/software/
+EXTRACT_SUFX=	.tar.Z
+
+MAINTAINER=	chuynh@biolateral.com.au
+
+MAN1=		tRNAscan-SE.1
+
+#
+# have to install before testing as path to data files is hardcoded
+#
+post-install:
+		@ cd ${WRKSRC} && $(MAKE) testrun
+.if !defined(NOPORTDOCS)
+	@${MKDIR} ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/Manual.ps ${DOCSDIR}
+.endif
+
+.include <bsd.port.mk>
diff --git a/biology/tRNAscan-SE/distinfo b/biology/tRNAscan-SE/distinfo
new file mode 100644
index 000000000000..d9f0e767d7c4
--- /dev/null
+++ b/biology/tRNAscan-SE/distinfo
@@ -0,0 +1 @@
+MD5 (tRNAscan-SE-1.21.tar.Z) = 8bdb481fbfc46836bf28f637eb96d306
diff --git a/biology/tRNAscan-SE/files/patch-aa b/biology/tRNAscan-SE/files/patch-aa
new file mode 100644
index 000000000000..82f9a3b420a0
--- /dev/null
+++ b/biology/tRNAscan-SE/files/patch-aa
@@ -0,0 +1,35 @@
+--- 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-comment b/biology/tRNAscan-SE/pkg-comment
new file mode 100644
index 000000000000..92cdd3eff0e5
--- /dev/null
+++ b/biology/tRNAscan-SE/pkg-comment
@@ -0,0 +1 @@
+An improved tool for transfer RNA detection
diff --git a/biology/tRNAscan-SE/pkg-descr b/biology/tRNAscan-SE/pkg-descr
new file mode 100644
index 000000000000..008e02d08a16
--- /dev/null
+++ b/biology/tRNAscan-SE/pkg-descr
@@ -0,0 +1,10 @@
+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/
diff --git a/biology/tRNAscan-SE/pkg-plist b/biology/tRNAscan-SE/pkg-plist
new file mode 100644
index 000000000000..06992dc3d94b
--- /dev/null
+++ b/biology/tRNAscan-SE/pkg-plist
@@ -0,0 +1,26 @@
+bin/tRNAscan-SE
+bin/eufindtRNA
+bin/coves-SE
+bin/covels-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%%share/doc/tRNAscan-SE/Manual.ps
+%%PORTDOCS%%@dirrm share/doc/tRNAscan-SE