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.

5 files changed, 208 insertions, 0 deletions

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