mummer4: import mummer-4.0.0rc1 (4.0.0.20201002) as wip/mummer4

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

Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <brook%nmsu.edu@localhost>
Pushed By:	brook
Date:		Mon Jun 21 13:58:31 2021 -0600
Changeset:	d03b59ccad278ef4135a9cf5b231f3fa057cc342

Modified Files:
	Makefile
Added Files:
	mummer4/DESCR
	mummer4/Makefile
	mummer4/PLIST
	mummer4/distinfo

Log Message:
mummer4: import mummer-4.0.0rc1 (4.0.0.20201002) as wip/mummer4

MUMmer is a versatile alignment tool for DNA and protein sequences.

MUMmer is a system for rapidly aligning DNA and protein sequences. The
nucmer aligner in the current version (release 4.x) can align two
mammalian genomes in about 3 hours on a typical 32+ core workstation
with 64+Gb RAM; smaller genomes such as bacteria or small eukaryotes
are aligned in seconds or minutes. The promer utility generates
alignments based upon the six-frame translations of both input
sequences. promer permits the alignment of genomes for which the
proteins are similar but the DNA sequence is too divergent to detect
similarity. See the nucmer and promer readme files in the "docs/"
subdirectory for more details. MUMmer is open source, and we ask that
you cite our most recent paper in any publications that use this
system:

Marcais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin
A. MUMmer4: A fast and versatile genome alignment system. PLoS
computational biology. 2018 Jan 26;14(1):e1005944.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=d03b59ccad278ef4135a9cf5b231f3fa057cc342

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

diffstat:
 Makefile         |  1 +
 mummer4/DESCR    | 18 ++++++++++++++++
 mummer4/Makefile | 24 +++++++++++++++++++++
 mummer4/PLIST    | 63 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 mummer4/distinfo |  6 ++++++
 5 files changed, 112 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 008b01385d..f14085c4ed 100644
--- a/Makefile
+++ b/Makefile
@@ -2436,6 +2436,7 @@ SUBDIR+=	multisync-palm
 SUBDIR+=	multisync-syncml
 SUBDIR+=	multisync-syncml-moto
 SUBDIR+=	multitail
+SUBDIR+=	mummer4
 SUBDIR+=	munge
 SUBDIR+=	muparser
 SUBDIR+=	mupen64plus
diff --git a/mummer4/DESCR b/mummer4/DESCR
new file mode 100644
index 0000000000..7ca37775cc
--- /dev/null
+++ b/mummer4/DESCR
@@ -0,0 +1,18 @@
+MUMmer is a versatile alignment tool for DNA and protein sequences.
+
+MUMmer is a system for rapidly aligning DNA and protein sequences. The
+nucmer aligner in the current version (release 4.x) can align two
+mammalian genomes in about 3 hours on a typical 32+ core workstation
+with 64+Gb RAM; smaller genomes such as bacteria or small eukaryotes
+are aligned in seconds or minutes. The promer utility generates
+alignments based upon the six-frame translations of both input
+sequences. promer permits the alignment of genomes for which the
+proteins are similar but the DNA sequence is too divergent to detect
+similarity. See the nucmer and promer readme files in the "docs/"
+subdirectory for more details. MUMmer is open source, and we ask that
+you cite our most recent paper in any publications that use this
+system:
+
+Marcais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin
+A. MUMmer4: A fast and versatile genome alignment system. PLoS
+computational biology. 2018 Jan 26;14(1):e1005944.
diff --git a/mummer4/Makefile b/mummer4/Makefile
new file mode 100644
index 0000000000..f8ef19f09c
--- /dev/null
+++ b/mummer4/Makefile
@@ -0,0 +1,24 @@
+# $NetBSD$
+
+GITHUB_PROJECT=	mummer
+DISTNAME=	mummer-4.0.0rc1
+PKGNAME=	mummer4-4.0.0.20201002
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=mummer4/}
+GITHUB_RELEASE=	v4.0.0rc1
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/mummer4/mummer/
+COMMENT=	Versatile alignment tool for DNA and protein sequences
+LICENSE=	artistic
+
+GNU_CONFIGURE=	yes
+USE_LIBTOOL=	yes
+USE_TOOLS+=	gmake perl:run pkg-config
+USE_LANGUAGES=	c c++
+
+CONFIGURE_ENV+=	PERL=${PERL5}
+
+PKGCONFIG_OVERRIDE+=	mummer.pc.in
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/mummer4/PLIST b/mummer4/PLIST
new file mode 100644
index 0000000000..d88a4e4d3d
--- /dev/null
+++ b/mummer4/PLIST
@@ -0,0 +1,63 @@
+@comment $NetBSD$
+bin/annotate
+bin/combineMUMs
+bin/delta-filter
+bin/delta2vcf
+bin/dnadiff
+bin/exact-tandems
+bin/mummer
+bin/mummerplot
+bin/nucmer
+bin/promer
+bin/repeat-match
+bin/show-aligns
+bin/show-coords
+bin/show-diff
+bin/show-snps
+bin/show-tiling
+include/${PKGNAME}/include/compactsufsort/compactsufsort.hpp
+include/${PKGNAME}/include/compactsufsort/compactsufsort_imp.hpp
+include/${PKGNAME}/include/compactsufsort/const_iterator_traits.hpp
+include/${PKGNAME}/include/compactsufsort/divsufsort_private.h
+include/${PKGNAME}/include/compactsufsort/said_traits.hpp
+include/${PKGNAME}/include/compactsufsort/sssort_imp.hpp
+include/${PKGNAME}/include/compactsufsort/trsort_imp.hpp
+include/${PKGNAME}/include/jellyfish/circular_buffer.hpp
+include/${PKGNAME}/include/jellyfish/cooperative_pool2.hpp
+include/${PKGNAME}/include/jellyfish/cpp_array.hpp
+include/${PKGNAME}/include/jellyfish/divisor.hpp
+include/${PKGNAME}/include/jellyfish/stream_manager.hpp
+include/${PKGNAME}/include/jellyfish/whole_sequence_parser.hpp
+include/${PKGNAME}/include/mt_skip_list/common.hpp
+include/${PKGNAME}/include/mt_skip_list/set.hpp
+include/${PKGNAME}/include/mummer/48bit_index.hpp
+include/${PKGNAME}/include/mummer/48bit_iterator.hpp
+include/${PKGNAME}/include/mummer/const_iterator_traits.hpp
+include/${PKGNAME}/include/mummer/delta.hh
+include/${PKGNAME}/include/mummer/dset.hpp
+include/${PKGNAME}/include/mummer/fasta.hpp
+include/${PKGNAME}/include/mummer/mgaps.hh
+include/${PKGNAME}/include/mummer/nucmer.hpp
+include/${PKGNAME}/include/mummer/openmp_qsort.hpp
+include/${PKGNAME}/include/mummer/postnuc.hh
+include/${PKGNAME}/include/mummer/redirect_to_pager.hpp
+include/${PKGNAME}/include/mummer/sparseSA.hpp
+include/${PKGNAME}/include/mummer/sparseSA_imp.hpp
+include/${PKGNAME}/include/mummer/sw_align.hh
+include/${PKGNAME}/include/mummer/sw_alignscore.hh
+include/${PKGNAME}/include/mummer/tigrinc.hh
+include/${PKGNAME}/include/mummer/timer.hpp
+include/${PKGNAME}/include/mummer/translate.hh
+include/${PKGNAME}/include/thread_pipe.hpp
+include/${PKGNAME}/include/thread_pipe/circular_buffer.hpp
+include/${PKGNAME}/include/thread_pipe/cooperative_pool2.hpp
+include/${PKGNAME}/include/thread_pipe/divisor.hpp
+include/${PKGNAME}/include/thread_pipe/traits.hpp
+lib/libumdmummer.la
+lib/mummer/Foundation.pm
+lib/mummer/tandem-repeat.awk
+lib/pkgconfig/mummer.pc
+libexec/mummer/mgaps
+libexec/mummer/postnuc
+libexec/mummer/postpro
+libexec/mummer/prepro
diff --git a/mummer4/distinfo b/mummer4/distinfo
new file mode 100644
index 0000000000..3a42a4c90d
--- /dev/null
+++ b/mummer4/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (mummer-4.0.0rc1.tar.gz) = 7f2c1a8ac71ade96e7c47fd81184aee04c20221c
+RMD160 (mummer-4.0.0rc1.tar.gz) = 6242cd846c7b2e3f39dbaa2b0ec893979644291b
+SHA512 (mummer-4.0.0rc1.tar.gz) = b120d80a540f62bf024b5a3f8c9fc65f3963119ed586292f3dce4b68287e4a31a54ec399dece4f87dafa171ff1e72a5ba8b452f70bd77d05efaaa088dcbd764b
+Size (mummer-4.0.0rc1.tar.gz) = 967486 bytes