Import /home/bacon/Pkgsrc/pkgsrc-2016Q1/wip/gmap gmap-2014.07.04 as wip/ gmap.

[Jason Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed May 11 15:25:11 2016 -0500
Changeset:	1b1f2fa027f512ff966a6dbcb977888c055770ac

Added Files:
	gmap/DESCR
	gmap/Makefile
	gmap/PLIST
	gmap/TODO
	gmap/buildlink3.mk
	gmap/distinfo

Log Message:
Import /home/bacon/Pkgsrc/pkgsrc-2016Q1/wip/gmap
gmap-2014.07.04 as wip/gmap.

A standalone program for mapping and aligning cDNA sequences to a
genome. The program maps and aligns a single sequence with minimal
startup time and memory requirements, and provides fast batch
processing of large sequence sets. The program generates accurate
gene structures, even in the presence of substantial polymorphisms
and sequence errors, without using probabilistic splice site models.
Methodology underlying the program includes a minimal sampling
strategy for genomic mapping, oligomer chaining for approximate
alignment, sandwich DP for splice site detection, and microexon
identification with statistical significance testing.

WWW: http://www.gene.com/share/gmap

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=1b1f2fa027f512ff966a6dbcb977888c055770ac

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 gmap/DESCR         | 12 ++++++++++++
 gmap/Makefile      | 34 ++++++++++++++++++++++++++++++++++
 gmap/PLIST         | 35 +++++++++++++++++++++++++++++++++++
 gmap/TODO          |  1 +
 gmap/buildlink3.mk | 22 ++++++++++++++++++++++
 gmap/distinfo      |  6 ++++++
 6 files changed, 110 insertions(+)

diffs:
diff --git a/gmap/DESCR b/gmap/DESCR
new file mode 100644
index 0000000..d09d51f
--- /dev/null
+++ b/gmap/DESCR
@@ -0,0 +1,12 @@
+A standalone program for mapping and aligning cDNA sequences to a
+genome. The program maps and aligns a single sequence with minimal
+startup time and memory requirements, and provides fast batch
+processing of large sequence sets. The program generates accurate
+gene structures, even in the presence of substantial polymorphisms
+and sequence errors, without using probabilistic splice site models.
+Methodology underlying the program includes a minimal sampling
+strategy for genomic mapping, oligomer chaining for approximate
+alignment, sandwich DP for splice site detection, and microexon
+identification with statistical significance testing.
+
+WWW: http://www.gene.com/share/gmap
diff --git a/gmap/Makefile b/gmap/Makefile
new file mode 100644
index 0000000..7635ac1
--- /dev/null
+++ b/gmap/Makefile
@@ -0,0 +1,34 @@
+# $NetBSD$
+
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+PKGNAME=	gmap-${PORTVERSION}
+DISTNAME=	gmap-${PORTVERSION:C|\.|-|g}
+DISTFILES=	gmap-gsnap-${PORTVERSION:C|\.|-|g}${EXTRACT_SUFX}
+CATEGORIES=	biology
+MASTER_SITES=	http://research-pub.gene.com/gmap/src/
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+
+COMMENT=	Genomic Mapping and Alignment Program for mRNA and EST Sequences
+#LICENSE=	
+
+# Pessimistic assumption.  Test and change if possible.
+# MAKE_JOBS_SAFE=	no
+
+ONLY_FOR_PLATFORM=	
+
+# FIXME: Add shebang fixes for perl scripts
+
+# Just assuming C and C++: Adjust this!
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	gmake
+GNU_CONFIGURE=	yes
+
+PORTVERSION=	2014.07.04
+DATADIR=	${PREFIX}/share/gmap
+DOCSDIR=	${PREFIX}/share/doc/gmap
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/gmap/PLIST b/gmap/PLIST
new file mode 100644
index 0000000..43e9126
--- /dev/null
+++ b/gmap/PLIST
@@ -0,0 +1,35 @@
+@comment $NetBSD$
+bin/atoiindex
+bin/cmetindex
+bin/dbsnp_iit
+bin/ensembl_genes
+bin/fa_coords
+bin/get-genome
+bin/gff3_genes
+bin/gff3_introns
+bin/gff3_splicesites
+bin/gmap
+bin/gmap_build
+bin/gmap_compress
+bin/gmap_process
+bin/gmap_reassemble
+bin/gmap_uncompress
+bin/gmapindex
+bin/gmapl
+bin/gsnap
+bin/gsnapl
+bin/gtf_genes
+bin/gtf_introns
+bin/gtf_splicesites
+bin/gvf_iit
+bin/iit_dump
+bin/iit_get
+bin/iit_store
+bin/md_coords
+bin/psl_genes
+bin/psl_introns
+bin/psl_splicesites
+bin/snpindex
+bin/uniqscan
+bin/uniqscanl
+bin/vcf_iit
diff --git a/gmap/TODO b/gmap/TODO
new file mode 100644
index 0000000..b687356
--- /dev/null
+++ b/gmap/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/gmap/buildlink3.mk b/gmap/buildlink3.mk
new file mode 100644
index 0000000..a583f83
--- /dev/null
+++ b/gmap/buildlink3.mk
@@ -0,0 +1,22 @@
+# $NetBSD$
+# XXX
+# XXX This file was created automatically using createbuildlink-3.16.
+# XXX After this file has been verified as correct, the comment lines
+# XXX beginning with "XXX" should be removed.  Please do not commit
+# XXX unverified buildlink3.mk files.
+# XXX
+# XXX Packages that only install static libraries or headers should
+# XXX include the following line:
+# XXX
+# XXX	BUILDLINK_DEPMETHOD.gmap?=	build
+
+BUILDLINK_TREE+=	gmap
+
+.if !defined(GMAP_BUILDLINK3_MK)
+GMAP_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.gmap+=	gmap>=2014.07.04
+BUILDLINK_PKGSRCDIR.gmap?=	../../wip/gmap
+.endif	# GMAP_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-gmap
diff --git a/gmap/distinfo b/gmap/distinfo
new file mode 100644
index 0000000..0035ed4
--- /dev/null
+++ b/gmap/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (gmap-gsnap-2014-07-04.tar.gz) = 247742abe8ea23efe6d839686e8a84ff1ea1331c
+RMD160 (gmap-gsnap-2014-07-04.tar.gz) = 0634baeb6c273c0721f7f600ed64005bc3d88d4c
+SHA512 (gmap-gsnap-2014-07-04.tar.gz) = 2f505e2a4c17d9d126f5cb199cf5e7cc539695e017c0f71b680f6db08f3521e7618220a9c9a8abf592e509c11053cc8ba19c7d7fb485855c7dbd6960b3bc3631
+Size (gmap-gsnap-2014-07-04.tar.gz) = 3977454 bytes