diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/genesplicer/DESCR | 4 | ||||
| -rw-r--r-- | biology/genesplicer/Makefile | 30 | ||||
| -rw-r--r-- | biology/genesplicer/PLIST | 148 | ||||
| -rw-r--r-- | biology/genesplicer/distinfo | 5 | ||||
| -rw-r--r-- | biology/genesplicer/patches/patch-aa | 21 |
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 |