diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/tRNAscan-SE/Makefile | 28 | ||||
| -rw-r--r-- | biology/tRNAscan-SE/distinfo | 1 | ||||
| -rw-r--r-- | biology/tRNAscan-SE/files/patch-aa | 35 | ||||
| -rw-r--r-- | biology/tRNAscan-SE/pkg-comment | 1 | ||||
| -rw-r--r-- | biology/tRNAscan-SE/pkg-descr | 10 | ||||
| -rw-r--r-- | biology/tRNAscan-SE/pkg-plist | 26 |
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 |