[pkgsrc/trunk]: pkgsrc/biology/genesplicer Initial import of genesplicer, one...

To: pkgsrc-changes-hg%NetBSD.org@localhost
Subject: [pkgsrc/trunk]: pkgsrc/biology/genesplicer Initial import of genesplicer, one...
From: jschauma <jschauma%pkgsrc.org@localhost>
Date: Wed, 13 Oct 2021 23:03:28 +0000
details:   https://anonhg.NetBSD.org/pkgsrc/rev/f668ce7faab1
branches:  trunk
changeset: 462297:f668ce7faab1
user:      jschauma <jschauma%pkgsrc.org@localhost>
date:      Tue Sep 30 01:57:08 2003 +0000

description:
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.

diffstat:

 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(+), 0 deletions(-)

diffs (228 lines):

diff -r 6fcddbd22eaa -r f668ce7faab1 biology/genesplicer/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/genesplicer/DESCR Tue Sep 30 01:57:08 2003 +0000
@@ -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 -r 6fcddbd22eaa -r f668ce7faab1 biology/genesplicer/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/genesplicer/Makefile      Tue Sep 30 01:57:08 2003 +0000
@@ -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@localhost
+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 -r 6fcddbd22eaa -r f668ce7faab1 biology/genesplicer/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/genesplicer/PLIST Tue Sep 30 01:57:08 2003 +0000
@@ -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 -r 6fcddbd22eaa -r f668ce7faab1 biology/genesplicer/distinfo
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/genesplicer/distinfo      Tue Sep 30 01:57:08 2003 +0000
@@ -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 -r 6fcddbd22eaa -r f668ce7faab1 biology/genesplicer/patches/patch-aa
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/genesplicer/patches/patch-aa      Tue Sep 30 01:57:08 2003 +0000
@@ -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
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