'Add smithwaterman: Smith-waterman-gotoh alignment algorithm'

[Jason Bacon <bacon@centosdev.local>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon@centosdev.local>
Pushed By:	outpaddling
Date:		Thu Mar 30 20:17:52 2017 -0500
Changeset:	8de66c938f26038b41c77559fd7cc3adb4b6503d

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

Log Message:
'Add smithwaterman: 	Smith-waterman-gotoh alignment algorithm'

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=8de66c938f26038b41c77559fd7cc3adb4b6503d

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

diffstat:
 Makefile                    |  1 +
 smithwaterman/DESCR         |  1 +
 smithwaterman/Makefile      | 27 +++++++++++++++++++++++++++
 smithwaterman/PLIST         | 12 ++++++++++++
 smithwaterman/TODO          |  1 +
 smithwaterman/buildlink3.mk | 12 ++++++++++++
 smithwaterman/distinfo      |  6 ++++++
 7 files changed, 60 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 471d447df5..1ecfbea75e 100644
--- a/Makefile
+++ b/Makefile
@@ -3991,6 +3991,7 @@ SUBDIR+=	smallbasic
 SUBDIR+=	smallbasic-gui
 SUBDIR+=	smap
 SUBDIR+=	smc
+SUBDIR+=	smithwaterman
 SUBDIR+=	smplayer
 SUBDIR+=	smproxy
 SUBDIR+=	smstools
diff --git a/smithwaterman/DESCR b/smithwaterman/DESCR
new file mode 100644
index 0000000000..62ebfdcb02
--- /dev/null
+++ b/smithwaterman/DESCR
@@ -0,0 +1 @@
+Smith-waterman-gotoh alignment algorithm.
diff --git a/smithwaterman/Makefile b/smithwaterman/Makefile
new file mode 100644
index 0000000000..fd4cb5c706
--- /dev/null
+++ b/smithwaterman/Makefile
@@ -0,0 +1,27 @@
+# $NetBSD$
+#
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+DISTNAME=	smithwaterman-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=outpaddling/}
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+HOMEPAGE=	https://github.com/ekg/smithwaterman
+COMMENT=	Smith-waterman-gotoh alignment algorithm
+LICENSE=	gnu-gpl-v2
+
+# Pessimistic assumption.  Test and change if possible.
+# MAKE_JOBS_SAFE=	no
+
+# Just assuming C and C++: Adjust this!
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	gmake
+INSTALL_TARGET=	install-strip
+GITHUB_TAG=	${PORTVERSION}
+
+PORTVERSION=	8e667291798b785d698f0875e58da2710d740567
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/smithwaterman/PLIST b/smithwaterman/PLIST
new file mode 100644
index 0000000000..5c2c743171
--- /dev/null
+++ b/smithwaterman/PLIST
@@ -0,0 +1,12 @@
+@comment $NetBSD$
+bin/smithwaterman
+include/smithwaterman/BandedSmithWaterman.h
+include/smithwaterman/IndelAllele.h
+include/smithwaterman/LeftAlign.h
+include/smithwaterman/Mosaik.h
+include/smithwaterman/Repeats.h
+include/smithwaterman/SmithWatermanGotoh.h
+include/smithwaterman/convert.h
+include/smithwaterman/disorder.h
+lib/libsw.a
+lib/libsw.so.1
diff --git a/smithwaterman/TODO b/smithwaterman/TODO
new file mode 100644
index 0000000000..b687356e6b
--- /dev/null
+++ b/smithwaterman/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/smithwaterman/buildlink3.mk b/smithwaterman/buildlink3.mk
new file mode 100644
index 0000000000..cd68d9fbff
--- /dev/null
+++ b/smithwaterman/buildlink3.mk
@@ -0,0 +1,12 @@
+# $NetBSD$
+
+BUILDLINK_TREE+=	smithwaterman
+
+.if !defined(SMITHWATERMAN_BUILDLINK3_MK)
+SMITHWATERMAN_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.smithwaterman+=	smithwaterman>=8e667291798b785d698f0875e58da2710d740567
+BUILDLINK_PKGSRCDIR.smithwaterman?=	../../wip/smithwaterman
+.endif	# SMITHWATERMAN_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-smithwaterman
diff --git a/smithwaterman/distinfo b/smithwaterman/distinfo
new file mode 100644
index 0000000000..82b08fd35b
--- /dev/null
+++ b/smithwaterman/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (smithwaterman-8e667291798b785d698f0875e58da2710d740567-8e667291798b785d698f0875e58da2710d740567.tar.gz) = 0057f7535fb87c6dc0b7c8ba5870bff6a43d520f
+RMD160 (smithwaterman-8e667291798b785d698f0875e58da2710d740567-8e667291798b785d698f0875e58da2710d740567.tar.gz) = 07bcff1ed35aba893b94cfa22f7e4594d0b2d167
+SHA512 (smithwaterman-8e667291798b785d698f0875e58da2710d740567-8e667291798b785d698f0875e58da2710d740567.tar.gz) = 3777fb7cfa107072ea2831344449e9bdb897d5006121063d5104863c4655f4b6c525ed135d5ccdc48d1f04e9281c3907c4344b52b9e1349e43f4b508a97a3e6c
+Size (smithwaterman-8e667291798b785d698f0875e58da2710d740567-8e667291798b785d698f0875e58da2710d740567.tar.gz) = 38774 bytes