From f4364c13ef2fe0062e235f1e1f61c6e676e9b195 Mon Sep 17 00:00:00 2001 From: jschauma Date: Tue, 30 Sep 2003 01:57:08 +0000 Subject: Initial import of genesplicer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. GeneSplicer is a fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and rice. --- biology/genesplicer/DESCR | 4 + biology/genesplicer/Makefile | 30 +++++++ biology/genesplicer/PLIST | 148 +++++++++++++++++++++++++++++++++++ biology/genesplicer/distinfo | 5 ++ biology/genesplicer/patches/patch-aa | 21 +++++ 5 files changed, 208 insertions(+) create mode 100644 biology/genesplicer/DESCR create mode 100644 biology/genesplicer/Makefile create mode 100644 biology/genesplicer/PLIST create mode 100644 biology/genesplicer/distinfo create mode 100644 biology/genesplicer/patches/patch-aa (limited to 'biology') diff --git a/biology/genesplicer/DESCR b/biology/genesplicer/DESCR new file mode 100644 index 00000000000..c8999a5aeed --- /dev/null +++ b/biology/genesplicer/DESCR @@ -0,0 +1,4 @@ +GeneSplicer is a fast, flexible system for detecting splice sites in the +genomic DNA of various eukaryotes. The system has been trained and tested +successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, +Drosophila, and rice. diff --git a/biology/genesplicer/Makefile b/biology/genesplicer/Makefile new file mode 100644 index 00000000000..04175e10d3e --- /dev/null +++ b/biology/genesplicer/Makefile @@ -0,0 +1,30 @@ +# $NetBSD: Makefile,v 1.1.1.1 2003/09/30 01:57:08 jschauma Exp $ +# + +DISTNAME= GeneSplicer +PKGNAME= genesplicer-20030403 +WRKSRC= ${WRKDIR}/GeneSplicer/sources +CATEGORIES= biology +MASTER_SITES= ftp://ftp.tigr.org/pub/software/GeneSplicer/ + +MAINTAINER= hdp@cs.nmsu.edu +HOMEPAGE= ftp://ftp.tigr.org/pub/software/GeneSplicer/ +COMMENT= Computational Method for Splice Site Prediction + +EXDIR= ${PREFIX}/share/examples/genesplicer +EXAMPLES= arabidopsis drosophila malaria pyoelii human rice \ + training_data_sets/Arabidopsis \ + training_data_sets/Human +MAKEFILE= makefile +USE_BUILDLINK2= yes + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/genesplicer ${PREFIX}/bin + ${INSTALL_DATA_DIR} ${EXDIR} +.for DOC in readme fasta.example fasta.results + ${INSTALL_DATA} ${WRKSRC}/${DOC} ${EXDIR} +.endfor + cd ${WRKSRC}/../ && ${PAX} -rw ${EXAMPLES} ${EXDIR}/ + +.include "../../mk/bsd.pkg.mk" + diff --git a/biology/genesplicer/PLIST b/biology/genesplicer/PLIST new file mode 100644 index 00000000000..d3f97e4560c --- /dev/null +++ b/biology/genesplicer/PLIST @@ -0,0 +1,148 @@ +@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/30 01:57:09 jschauma Exp $ +bin/genesplicer +share/examples/genesplicer/arabidopsis/acc1.mar +share/examples/genesplicer/arabidopsis/acc15 +share/examples/genesplicer/arabidopsis/acc16 +share/examples/genesplicer/arabidopsis/acc22 +share/examples/genesplicer/arabidopsis/acc24 +share/examples/genesplicer/arabidopsis/acc25 +share/examples/genesplicer/arabidopsis/acc26 +share/examples/genesplicer/arabidopsis/acc6 +share/examples/genesplicer/arabidopsis/acc7 +share/examples/genesplicer/arabidopsis/acc8 +share/examples/genesplicer/arabidopsis/config_file +share/examples/genesplicer/arabidopsis/don1.mar +share/examples/genesplicer/arabidopsis/don13 +share/examples/genesplicer/arabidopsis/don14 +share/examples/genesplicer/arabidopsis/don19 +share/examples/genesplicer/arabidopsis/don20 +share/examples/genesplicer/arabidopsis/don23 +share/examples/genesplicer/arabidopsis/don24 +share/examples/genesplicer/arabidopsis/don7 +share/examples/genesplicer/arabidopsis/don8 +share/examples/genesplicer/arabidopsis/exons.dat +share/examples/genesplicer/arabidopsis/f.acc +share/examples/genesplicer/arabidopsis/f.don +share/examples/genesplicer/arabidopsis/outex +share/examples/genesplicer/arabidopsis/outin +share/examples/genesplicer/arabidopsis/score_ex.acc +share/examples/genesplicer/arabidopsis/score_ex.don +share/examples/genesplicer/arabidopsis/score_in.acc +share/examples/genesplicer/arabidopsis/score_in.don +share/examples/genesplicer/arabidopsis/seqs +share/examples/genesplicer/drosophila/acc1.mar +share/examples/genesplicer/drosophila/acc2 +share/examples/genesplicer/drosophila/acc3 +share/examples/genesplicer/drosophila/acc4 +share/examples/genesplicer/drosophila/config_file +share/examples/genesplicer/drosophila/don1.mar +share/examples/genesplicer/drosophila/don2 +share/examples/genesplicer/drosophila/don4 +share/examples/genesplicer/drosophila/don5 +share/examples/genesplicer/drosophila/don6 +share/examples/genesplicer/drosophila/exons.dat +share/examples/genesplicer/drosophila/f.acc +share/examples/genesplicer/drosophila/f.don +share/examples/genesplicer/drosophila/false.filter.acc +share/examples/genesplicer/drosophila/false.filter.don +share/examples/genesplicer/drosophila/false.nofilter.acc +share/examples/genesplicer/drosophila/false.nofilter.don +share/examples/genesplicer/drosophila/outex +share/examples/genesplicer/drosophila/outin +share/examples/genesplicer/drosophila/score_ex.acc +share/examples/genesplicer/drosophila/score_ex.don +share/examples/genesplicer/drosophila/score_in.acc +share/examples/genesplicer/drosophila/score_in.don +share/examples/genesplicer/drosophila/seqs +share/examples/genesplicer/fasta.example +share/examples/genesplicer/fasta.results +share/examples/genesplicer/human/acc1.mar +share/examples/genesplicer/human/acc13 +share/examples/genesplicer/human/acc14 +share/examples/genesplicer/human/acc19 +share/examples/genesplicer/human/acc20 +share/examples/genesplicer/human/acc25 +share/examples/genesplicer/human/acc26 +share/examples/genesplicer/human/acc32 +share/examples/genesplicer/human/acc33 +share/examples/genesplicer/human/acc34 +share/examples/genesplicer/human/acc7 +share/examples/genesplicer/human/acc8 +share/examples/genesplicer/human/chgd.fasta +share/examples/genesplicer/human/config_file +share/examples/genesplicer/human/don1.mar +share/examples/genesplicer/human/don10 +share/examples/genesplicer/human/don15 +share/examples/genesplicer/human/don16 +share/examples/genesplicer/human/don19 +share/examples/genesplicer/human/don2 +share/examples/genesplicer/human/don20 +share/examples/genesplicer/human/don23 +share/examples/genesplicer/human/don24 +share/examples/genesplicer/human/don9 +share/examples/genesplicer/human/embls.seq +share/examples/genesplicer/human/exons.dat +share/examples/genesplicer/human/exons.list +share/examples/genesplicer/human/f.acc +share/examples/genesplicer/human/f.don +share/examples/genesplicer/human/outex +share/examples/genesplicer/human/outin +share/examples/genesplicer/human/score_ex.acc +share/examples/genesplicer/human/score_ex.don +share/examples/genesplicer/human/score_in.acc +share/examples/genesplicer/human/score_in.don +share/examples/genesplicer/human/seqs +share/examples/genesplicer/malaria/acc1.mar +share/examples/genesplicer/malaria/config_file +share/examples/genesplicer/malaria/don1.mar +share/examples/genesplicer/malaria/f.acc +share/examples/genesplicer/malaria/f.don +share/examples/genesplicer/malaria/false.filter.acc +share/examples/genesplicer/malaria/false.filter.don +share/examples/genesplicer/malaria/false.nofilter.acc +share/examples/genesplicer/malaria/false.nofilter.don +share/examples/genesplicer/malaria/score_ex.acc +share/examples/genesplicer/malaria/score_ex.don +share/examples/genesplicer/malaria/score_in.acc +share/examples/genesplicer/malaria/score_in.don +share/examples/genesplicer/pyoelii/acc1 +share/examples/genesplicer/pyoelii/acc1.mar +share/examples/genesplicer/pyoelii/acc2 +share/examples/genesplicer/pyoelii/config_file +share/examples/genesplicer/pyoelii/don1 +share/examples/genesplicer/pyoelii/don1.mar +share/examples/genesplicer/pyoelii/don2 +share/examples/genesplicer/pyoelii/f.acc +share/examples/genesplicer/pyoelii/f.don +share/examples/genesplicer/pyoelii/outex +share/examples/genesplicer/pyoelii/outin +share/examples/genesplicer/pyoelii/score_ex.acc +share/examples/genesplicer/pyoelii/score_ex.don +share/examples/genesplicer/pyoelii/score_in.acc +share/examples/genesplicer/pyoelii/score_in.don +share/examples/genesplicer/readme +share/examples/genesplicer/rice/acc1.mar +share/examples/genesplicer/rice/config_file +share/examples/genesplicer/rice/don1.mar +share/examples/genesplicer/rice/exons.dat +share/examples/genesplicer/rice/f.acc +share/examples/genesplicer/rice/f.don +share/examples/genesplicer/rice/score_ex.acc +share/examples/genesplicer/rice/score_ex.don +share/examples/genesplicer/rice/score_in.acc +share/examples/genesplicer/rice/score_in.don +share/examples/genesplicer/rice/seqs +share/examples/genesplicer/training_data_sets/Arabidopsis/exons.dat.nohomologs +share/examples/genesplicer/training_data_sets/Arabidopsis/seqs.nohomologs +share/examples/genesplicer/training_data_sets/Human/exons.dat.nohomologs +share/examples/genesplicer/training_data_sets/Human/seqs.nohomologs +@dirrm share/examples/genesplicer/training_data_sets/Human +@dirrm share/examples/genesplicer/training_data_sets/Arabidopsis +@dirrm share/examples/genesplicer/training_data_sets +@dirrm share/examples/genesplicer/rice +@dirrm share/examples/genesplicer/pyoelii +@dirrm share/examples/genesplicer/malaria +@dirrm share/examples/genesplicer/human +@dirrm share/examples/genesplicer/drosophila +@dirrm share/examples/genesplicer/arabidopsis +@dirrm share/examples/genesplicer diff --git a/biology/genesplicer/distinfo b/biology/genesplicer/distinfo new file mode 100644 index 00000000000..76acc8909ed --- /dev/null +++ b/biology/genesplicer/distinfo @@ -0,0 +1,5 @@ +$NetBSD: distinfo,v 1.1.1.1 2003/09/30 01:57:09 jschauma Exp $ + +SHA1 (GeneSplicer.tar.gz) = 2be13d1a3ccb108e3e209ca5e66cd5a46e023198 +Size (GeneSplicer.tar.gz) = 9278730 bytes +SHA1 (patch-aa) = e5f9122422f23d124529f7aa7d632b299abcc827 diff --git a/biology/genesplicer/patches/patch-aa b/biology/genesplicer/patches/patch-aa new file mode 100644 index 00000000000..69eaecc68c7 --- /dev/null +++ b/biology/genesplicer/patches/patch-aa @@ -0,0 +1,21 @@ +$NetBSD: patch-aa,v 1.1.1.1 2003/09/30 01:57:09 jschauma Exp $ + +--- makefile.orig 2003-09-29 21:39:36.000000000 -0400 ++++ makefile 2003-09-29 21:40:57.000000000 -0400 +@@ -1,12 +1,12 @@ +-CC=g++ ++#CC=g++ + + all: genesplicer + + genesplicer: genesplicer.o sites.o +- $(CC) -o genesplicer genesplicer.o sites.o -lm ++ $(CXX) ${CXXFLAGS} -o genesplicer genesplicer.o sites.o ${LDFLAGS} -lm + + genesplicer.o: genesplicer.cpp +- $(CC) -c genesplicer.cpp ++ $(CXX) ${CXXFLAGS} -c genesplicer.cpp + + sites.o: sites.c +- $(CC) -c sites.c ++ $(CXX) ${CXXFLAGS} -c sites.c -- cgit v1.2.3