jellyfish2: Clean up and update MASTER_SITE

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Thu Apr 6 07:53:37 2017 -0500
Changeset:	d2784ec5edacd854a6367413f66c82bc3d68f82d

Modified Files:
	jellyfish2/Makefile
	jellyfish2/PLIST

Log Message:
jellyfish2: Clean up and update MASTER_SITE

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=d2784ec5edacd854a6367413f66c82bc3d68f82d

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

diffstat:
 jellyfish2/Makefile |  7 ++--
 jellyfish2/PLIST    | 96 ++++++++++++++++++++++++++---------------------------
 2 files changed, 51 insertions(+), 52 deletions(-)

diffs:
diff --git a/jellyfish2/Makefile b/jellyfish2/Makefile
index 3c62cb99a6..44712a48fc 100644
--- a/jellyfish2/Makefile
+++ b/jellyfish2/Makefile
@@ -7,7 +7,7 @@
 DISTNAME=	jellyfish-${PORTVERSION}
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=gmarcais/}
-MAINTAINER=	dsiercks%uwm.edu@localhost
+MAINTAINER=	bacon4000%gmail.com@localhost
 HOMEPAGE=	http://www.genome.umd.edu/jellyfish.html
 DISTNAME=	jellyfish-v${PORTVERSION}
 
@@ -15,11 +15,12 @@ COMMENT=	Fast, memory-efficient counting of k-mers in DNA
 LICENSE=	gnu-gpl-v3
 
 USE_TOOLS=	autoreconf autoconf automake
-# Just assuming C and C++: Adjust this!
 USE_LANGUAGES=	c c++
 USE_LIBTOOL=	yes
 GNU_CONFIGURE=	yes
 
+DEPENDS+=	yaggo>=0:../../wip/yaggo
+
 CFLAGS=		-fopenmp
 
 CXXFLAGS+=	-std=c++0x
@@ -27,10 +28,8 @@ CXXFLAGS+=	-std=c++0x
 WRKSRC=		${WRKDIR}/Jellyfish-${PORTVERSION}
 
 PORTVERSION=	2.2.6
-INSTALLATION_DIRS=	bin lib ${PKGMANDIR}/man1 share/doc share/examples
 
 pre-configure:
 	cd ${WRKSRC} && autoreconf -if
 
-# .include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/jellyfish2/PLIST b/jellyfish2/PLIST
index 33ef5ef792..d22b02928f 100644
--- a/jellyfish2/PLIST
+++ b/jellyfish2/PLIST
@@ -1,53 +1,53 @@
 @comment $NetBSD$
 bin/jellyfish
-include/${PKGNAME}/jellyfish/allocators_mmap.hpp
-include/${PKGNAME}/jellyfish/atomic_bits_array.hpp
-include/${PKGNAME}/jellyfish/atomic_field.hpp
-include/${PKGNAME}/jellyfish/atomic_gcc.hpp
-include/${PKGNAME}/jellyfish/backtrace.hpp
-include/${PKGNAME}/jellyfish/binary_dumper.hpp
-include/${PKGNAME}/jellyfish/bloom_common.hpp
-include/${PKGNAME}/jellyfish/bloom_counter2.hpp
-include/${PKGNAME}/jellyfish/bloom_filter.hpp
-include/${PKGNAME}/jellyfish/circular_buffer.hpp
-include/${PKGNAME}/jellyfish/compare_and_swap.hpp
-include/${PKGNAME}/jellyfish/cooperative_pool2.hpp
-include/${PKGNAME}/jellyfish/cooperative_pool.hpp
-include/${PKGNAME}/jellyfish/cpp_array.hpp
-include/${PKGNAME}/jellyfish/divisor.hpp
-include/${PKGNAME}/jellyfish/dumper.hpp
-include/${PKGNAME}/jellyfish/err.hpp
-include/${PKGNAME}/jellyfish/file_header.hpp
-include/${PKGNAME}/jellyfish/generator_manager.hpp
-include/${PKGNAME}/jellyfish/generic_file_header.hpp
-include/${PKGNAME}/jellyfish/hash_counter.hpp
-include/${PKGNAME}/jellyfish/int128.hpp
-include/${PKGNAME}/jellyfish/jellyfish.hpp
-include/${PKGNAME}/jellyfish/json.h
-include/${PKGNAME}/jellyfish/large_hash_array.hpp
-include/${PKGNAME}/jellyfish/large_hash_iterator.hpp
-include/${PKGNAME}/jellyfish/locks_pthread.hpp
-include/${PKGNAME}/jellyfish/mapped_file.hpp
-include/${PKGNAME}/jellyfish/mer_dna_bloom_counter.hpp
-include/${PKGNAME}/jellyfish/mer_dna.hpp
-include/${PKGNAME}/jellyfish/mer_heap.hpp
-include/${PKGNAME}/jellyfish/mer_iterator.hpp
-include/${PKGNAME}/jellyfish/mer_overlap_sequence_parser.hpp
-include/${PKGNAME}/jellyfish/mer_qual_iterator.hpp
-include/${PKGNAME}/jellyfish/misc.hpp
-include/${PKGNAME}/jellyfish/offsets_key_value.hpp
-include/${PKGNAME}/jellyfish/rectangular_binary_matrix.hpp
-include/${PKGNAME}/jellyfish/simple_circular_buffer.hpp
-include/${PKGNAME}/jellyfish/sorted_dumper.hpp
-include/${PKGNAME}/jellyfish/stdio_filebuf.hpp
-include/${PKGNAME}/jellyfish/storage.hpp
-include/${PKGNAME}/jellyfish/stream_iterator.hpp
-include/${PKGNAME}/jellyfish/stream_manager.hpp
-include/${PKGNAME}/jellyfish/text_dumper.hpp
-include/${PKGNAME}/jellyfish/thread_exec.hpp
-include/${PKGNAME}/jellyfish/time.hpp
-include/${PKGNAME}/jellyfish/token_ring.hpp
-include/${PKGNAME}/jellyfish/whole_sequence_parser.hpp
+include/jellyfish-2.2.6/jellyfish/allocators_mmap.hpp
+include/jellyfish-2.2.6/jellyfish/atomic_bits_array.hpp
+include/jellyfish-2.2.6/jellyfish/atomic_field.hpp
+include/jellyfish-2.2.6/jellyfish/atomic_gcc.hpp
+include/jellyfish-2.2.6/jellyfish/backtrace.hpp
+include/jellyfish-2.2.6/jellyfish/binary_dumper.hpp
+include/jellyfish-2.2.6/jellyfish/bloom_common.hpp
+include/jellyfish-2.2.6/jellyfish/bloom_counter2.hpp
+include/jellyfish-2.2.6/jellyfish/bloom_filter.hpp
+include/jellyfish-2.2.6/jellyfish/circular_buffer.hpp
+include/jellyfish-2.2.6/jellyfish/compare_and_swap.hpp
+include/jellyfish-2.2.6/jellyfish/cooperative_pool.hpp
+include/jellyfish-2.2.6/jellyfish/cooperative_pool2.hpp
+include/jellyfish-2.2.6/jellyfish/cpp_array.hpp
+include/jellyfish-2.2.6/jellyfish/divisor.hpp
+include/jellyfish-2.2.6/jellyfish/dumper.hpp
+include/jellyfish-2.2.6/jellyfish/err.hpp
+include/jellyfish-2.2.6/jellyfish/file_header.hpp
+include/jellyfish-2.2.6/jellyfish/generator_manager.hpp
+include/jellyfish-2.2.6/jellyfish/generic_file_header.hpp
+include/jellyfish-2.2.6/jellyfish/hash_counter.hpp
+include/jellyfish-2.2.6/jellyfish/int128.hpp
+include/jellyfish-2.2.6/jellyfish/jellyfish.hpp
+include/jellyfish-2.2.6/jellyfish/json.h
+include/jellyfish-2.2.6/jellyfish/large_hash_array.hpp
+include/jellyfish-2.2.6/jellyfish/large_hash_iterator.hpp
+include/jellyfish-2.2.6/jellyfish/locks_pthread.hpp
+include/jellyfish-2.2.6/jellyfish/mapped_file.hpp
+include/jellyfish-2.2.6/jellyfish/mer_dna.hpp
+include/jellyfish-2.2.6/jellyfish/mer_dna_bloom_counter.hpp
+include/jellyfish-2.2.6/jellyfish/mer_heap.hpp
+include/jellyfish-2.2.6/jellyfish/mer_iterator.hpp
+include/jellyfish-2.2.6/jellyfish/mer_overlap_sequence_parser.hpp
+include/jellyfish-2.2.6/jellyfish/mer_qual_iterator.hpp
+include/jellyfish-2.2.6/jellyfish/misc.hpp
+include/jellyfish-2.2.6/jellyfish/offsets_key_value.hpp
+include/jellyfish-2.2.6/jellyfish/rectangular_binary_matrix.hpp
+include/jellyfish-2.2.6/jellyfish/simple_circular_buffer.hpp
+include/jellyfish-2.2.6/jellyfish/sorted_dumper.hpp
+include/jellyfish-2.2.6/jellyfish/stdio_filebuf.hpp
+include/jellyfish-2.2.6/jellyfish/storage.hpp
+include/jellyfish-2.2.6/jellyfish/stream_iterator.hpp
+include/jellyfish-2.2.6/jellyfish/stream_manager.hpp
+include/jellyfish-2.2.6/jellyfish/text_dumper.hpp
+include/jellyfish-2.2.6/jellyfish/thread_exec.hpp
+include/jellyfish-2.2.6/jellyfish/time.hpp
+include/jellyfish-2.2.6/jellyfish/token_ring.hpp
+include/jellyfish-2.2.6/jellyfish/whole_sequence_parser.hpp
 lib/libjellyfish-2.0.la
 lib/pkgconfig/jellyfish-2.0.pc
 man/man1/jellyfish.1