Update jellyfish from jb-wip

[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 10:05:52 2016 -0500
Changeset:	2f77da432c3d8ce5ef3091cd9ef4353bce41f2cf

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

Log Message:
Update jellyfish from jb-wip

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=2f77da432c3d8ce5ef3091cd9ef4353bce41f2cf

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

diffstat:
 jellyfish/DESCR         |  2 --
 jellyfish/Makefile      | 39 ++++++++++++++++++---------------------
 jellyfish/PLIST         |  2 +-
 jellyfish/TODO          |  1 +
 jellyfish/buildlink3.mk | 12 +-----------
 jellyfish/distinfo      |  2 +-
 6 files changed, 22 insertions(+), 36 deletions(-)

diffs:
diff --git a/jellyfish/DESCR b/jellyfish/DESCR
index b174132..4b5859e 100644
--- a/jellyfish/DESCR
+++ b/jellyfish/DESCR
@@ -3,5 +3,3 @@ A k-mer is a substring of length k, and counting the occurrences of all such
 substrings is a central step in many analyses of DNA sequence. JELLYFISH can
 count k-mers quickly by using an efficient encoding of a hash table and by
 exploiting the "compare-and-swap" CPU instruction to increase parallelism.
-
-WWW: http://www.genome.umd.edu/jellyfish.html
diff --git a/jellyfish/Makefile b/jellyfish/Makefile
index 6ed2043..f40ef30 100644
--- a/jellyfish/Makefile
+++ b/jellyfish/Makefile
@@ -1,5 +1,5 @@
-# $NetBSD: Makefile,v 1.1 2015/01/28 16:36:28 outpaddling Exp $
-
+# $NetBSD$
+#
 ###########################################################
 #               Generated by fbsd2pkg                     #
 ###########################################################
@@ -7,46 +7,43 @@
 ###########################################################
 # Unconverted and partially converted FreeBSD port syntax:
 
-## Created by: Jason Bacon <jwbacon%tds.net@localhost>
-## $FreeBSD$
 ## Variable length arrays
 #USE_GCC=	yes
-#MAKE_JOBS_UNSAFE=yes
-#USE_LDCONFIG=	yes
-#LDFLAGS=	-lexecinfo
 ## GCC? -Wl,-rpath=${PREFIX}
 #post-stage:
 #	${MV} ${DESTDIR}${PREFIX}/lib/pkgconfig/* \
 #		${DESTDIR}${PREFIX}/libdata/pkgconfig
-#.include <bsd.port.mk>
 
-DISTNAME=	jellyfish-1.1.11
+DISTNAME=	jellyfish-${PORTVERSION}
 CATEGORIES=	biology
 MASTER_SITES=	http://www.cbcb.umd.edu/software/jellyfish/
 
-MAINTAINER=	jwbacon%tds.net@localhost
-
+MAINTAINER=	bacon4000%gmail.com@localhost
+HOMEPAGE=	http://www.genome.umd.edu/jellyfish.html
 COMMENT=	Fast, memory-efficient counting of k-mers in DNA
+# Double-check this
 LICENSE=	gnu-gpl-v3
 
-# Pessimistic assumption.  Test and change if possible.
-MAKE_JOBS_SAFE=	no
-
-ONLY_FOR_PLATFORM=	
+# Test and change if necessary.
+# MAKE_JOBS_SAFE=	no
 
 # Just assuming C and C++: Adjust this!
 USE_LANGUAGES=	c c++
+USE_TOOLS+=	gmake
+USE_LIBTOOL=	yes
 GNU_CONFIGURE=	yes
-DATADIR=	${PREFIX}/share/jellyfish
-DOCSDIR=	${PREFIX}/share/doc/jellyfish
+
+PORTVERSION=	1.1.11
 
 # Sets OPSYS, OS_VERSION, MACHINE_ARCH, etc..
-#.include "../../mk/bsd.prefs.mk"
+# .include "../../mk/bsd.prefs.mk"
 
 # Keep this if there are user-selectable options.
-#.include "options.mk"
+# .include "options.mk"
 
-# You may need this, especially if using do-install.
-#AUTO_MKDIRS=	yes
+# Specify which directories to create before install.
+# INSTALLATION_DIRS=	bin lib ${PKGMANDIR}/man1 share/doc share/examples
 
+# Linux doesn't have zlib in the base, so just in case...
+# .include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/jellyfish/PLIST b/jellyfish/PLIST
index 6a0c80d..f08ffd7 100644
--- a/jellyfish/PLIST
+++ b/jellyfish/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.1 2015/01/28 16:36:28 outpaddling Exp $
+@comment $NetBSD$
 bin/jellyfish
 include/${PKGNAME}/jellyfish/aligned_values_array.hpp
 include/${PKGNAME}/jellyfish/allocators_malloc.hpp
diff --git a/jellyfish/TODO b/jellyfish/TODO
new file mode 100644
index 0000000..b2e3b56
--- /dev/null
+++ b/jellyfish/TODO
@@ -0,0 +1 @@
+Clean up and test.
diff --git a/jellyfish/buildlink3.mk b/jellyfish/buildlink3.mk
index 5657c0a..4eb3981 100644
--- a/jellyfish/buildlink3.mk
+++ b/jellyfish/buildlink3.mk
@@ -1,14 +1,4 @@
-# $NetBSD: buildlink3.mk,v 1.1 2015/01/28 16:36:28 outpaddling Exp $
-# 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.jellyfish?=	build
+# $NetBSD$
 
 BUILDLINK_TREE+=	jellyfish
 
diff --git a/jellyfish/distinfo b/jellyfish/distinfo
index d4bd020..6e41bdc 100644
--- a/jellyfish/distinfo
+++ b/jellyfish/distinfo
@@ -1,4 +1,4 @@
-$NetBSD: distinfo,v 1.1 2015/01/28 16:36:28 outpaddling Exp $
+$NetBSD$
 
 SHA1 (jellyfish-1.1.11.tar.gz) = 8bd6a7b382e94d37adfddd916dec2b0e36f840fd
 RMD160 (jellyfish-1.1.11.tar.gz) = 30c4ed6d264cbe736ab9da977074f743998fb1d2