diff options
author | jschauma <jschauma> | 2003-09-30 01:57:08 +0000 |
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committer | jschauma <jschauma> | 2003-09-30 01:57:08 +0000 |
commit | 746509435a9a72d11bbaabb2bbc01ddb012d6bb2 (patch) | |
tree | 2825f07469a0e3ed7d2008b2167b6c1c00269bb9 | |
parent | 617cd88a3f84f237eac7a0563a2b642a07b92de0 (diff) | |
download | pkgsrc-746509435a9a72d11bbaabb2bbc01ddb012d6bb2.tar.gz |
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.
-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 |