SNAP: Import SNAP-0.0.0.20210910 (b90c63a) as wip/SNAP.

[Brook Milligan <brook%nmsu.edu@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <brook%nmsu.edu@localhost>
Pushed By:	brook
Date:		Mon Sep 13 12:51:26 2021 -0600
Changeset:	cbf7bd059e821061d1ed3cd2c84ed821676e1d08

Modified Files:
	Makefile
Added Files:
	SNAP/DESCR
	SNAP/Makefile
	SNAP/PLIST
	SNAP/distinfo

Log Message:
SNAP: Import SNAP-0.0.0.20210910 (b90c63a) as wip/SNAP.

SNAP is a general purpose gene finding program suitable for both
eukaryotic and prokaryotic genomes. SNAP is an acroynm for
Semi-HMM-based Nucleic Acid Parser.

Reference: Korf I. Gene finding in novel Genomes. BMC Bioinformatics
2004, 5:59

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=cbf7bd059e821061d1ed3cd2c84ed821676e1d08

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

diffstat:
 Makefile      |  1 +
 SNAP/DESCR    |  6 ++++++
 SNAP/Makefile | 33 +++++++++++++++++++++++++++++++++
 SNAP/PLIST    | 41 +++++++++++++++++++++++++++++++++++++++++
 SNAP/distinfo |  6 ++++++
 5 files changed, 87 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index b17c1e30eb..8ee7876b06 100644
--- a/Makefile
+++ b/Makefile
@@ -78,6 +78,7 @@ SUBDIR+=	R-wk
 SUBDIR+=	Radicale3
 SUBDIR+=	ReZound
 SUBDIR+=	RigelEngine
+SUBDIR+=	SNAP
 SUBDIR+=	SOGo5
 SUBDIR+=	Siesta
 SUBDIR+=	StepTalk
diff --git a/SNAP/DESCR b/SNAP/DESCR
new file mode 100644
index 0000000000..e8f8c9e267
--- /dev/null
+++ b/SNAP/DESCR
@@ -0,0 +1,6 @@
+SNAP is a general purpose gene finding program suitable for both
+eukaryotic and prokaryotic genomes. SNAP is an acroynm for
+Semi-HMM-based Nucleic Acid Parser.
+
+Reference: Korf I. Gene finding in novel Genomes. BMC Bioinformatics
+2004, 5:59
diff --git a/SNAP/Makefile b/SNAP/Makefile
new file mode 100644
index 0000000000..045088e1aa
--- /dev/null
+++ b/SNAP/Makefile
@@ -0,0 +1,33 @@
+# $NetBSD$
+
+GITHUB_PROJECT=	SNAP
+GITHUB_TAG=	b90c63a6a8af711323249c542d0587f20722712e
+DISTNAME=	master
+PKGNAME=	${GITHUB_PROJECT}-0.0.0.20210910
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=KorfLab/}
+EXTRACT_SUFX=	.zip
+DIST_SUBDIR=	${GITHUB_PROJECT}
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/KorfLab/SNAP/
+COMMENT=	Gene finding for prokaryotic and eukaryotic genomes
+LICENSE=	mit
+
+WRKSRC=		${WRKDIR}/SNAP-${GITHUB_TAG}
+USE_LANGUAGES+=	c
+USE_TOOLS+=	gmake pax
+BUILD_TARGET+=	default
+
+INSTALLATION_DIRS+=	bin share/SNAP/Zoe
+PROGRAMS=		fathom forge snap Zoe/zoe-loop
+HMMS=			README.md brugia ciona fly mosquito rice thale worm *.hmm
+
+do-install:
+.for f in ${PROGRAMS}
+	${INSTALL_PROGRAM} ${WRKSRC}/${f} ${DESTDIR}${PREFIX}/bin
+.endfor
+	cd ${WRKSRC}/HMM && ${PAX} -rw ${HMMS} ${DESTDIR}${PREFIX}/share/SNAP/Zoe
+	${CHMOD} a-w ${DESTDIR}${PREFIX}/share/SNAP/Zoe/*
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/SNAP/PLIST b/SNAP/PLIST
new file mode 100644
index 0000000000..d201d97acb
--- /dev/null
+++ b/SNAP/PLIST
@@ -0,0 +1,41 @@
+@comment $NetBSD$
+bin/fathom
+bin/forge
+bin/snap
+bin/zoe-loop
+share/SNAP/Zoe/A.gambiae.hmm
+share/SNAP/Zoe/A.mellifera.hmm
+share/SNAP/Zoe/A.thaliana.hmm
+share/SNAP/Zoe/Acanium.hmm
+share/SNAP/Zoe/At.hmm
+share/SNAP/Zoe/B.malayi.hmm
+share/SNAP/Zoe/B.mori.hmm
+share/SNAP/Zoe/C.elegans.hmm
+share/SNAP/Zoe/C.intestinalis.hmm
+share/SNAP/Zoe/Ce.hmm
+share/SNAP/Zoe/D.melanogaster.hmm
+share/SNAP/Zoe/Dm.hmm
+share/SNAP/Zoe/Nasonia.hmm
+share/SNAP/Zoe/O.sativa.hmm
+share/SNAP/Zoe/Os.hmm
+share/SNAP/Zoe/README.md
+share/SNAP/Zoe/brugia
+share/SNAP/Zoe/ciona
+share/SNAP/Zoe/fly
+share/SNAP/Zoe/ixodesA.hmm
+share/SNAP/Zoe/ixodesB.hmm
+share/SNAP/Zoe/mam39-ro.hmm
+share/SNAP/Zoe/mam39.hmm
+share/SNAP/Zoe/mam46-ro.hmm
+share/SNAP/Zoe/mam46.hmm
+share/SNAP/Zoe/mam54-ro.hmm
+share/SNAP/Zoe/mam54.hmm
+share/SNAP/Zoe/mamiso.hmm
+share/SNAP/Zoe/minimal.hmm
+share/SNAP/Zoe/mosquito
+share/SNAP/Zoe/nGASP.hmm
+share/SNAP/Zoe/nGASPr.hmm
+share/SNAP/Zoe/rice
+share/SNAP/Zoe/thale
+share/SNAP/Zoe/worm
+share/SNAP/Zoe/worm1.hmm
diff --git a/SNAP/distinfo b/SNAP/distinfo
new file mode 100644
index 0000000000..fb5c384755
--- /dev/null
+++ b/SNAP/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (SNAP/master-b90c63a6a8af711323249c542d0587f20722712e.zip) = a4795182d9cfce11bdd89360cfe07e5a155652cc
+RMD160 (SNAP/master-b90c63a6a8af711323249c542d0587f20722712e.zip) = 59b2e55c3fe14d329991c975d7b683213efc43fb
+SHA512 (SNAP/master-b90c63a6a8af711323249c542d0587f20722712e.zip) = e31335a95563b4944ced517aa1a03f58ebfbc126ec736a10ee12e59051ca947fb4f2492039a9f493c8e1bc1b74171286ec41fb1fc5f1a95abf427bd8a2bf51be
+Size (SNAP/master-b90c63a6a8af711323249c542d0587f20722712e.zip) = 743602 bytes