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