BSD Portsbiology/mummer 4.0.1 FreeBSD
Modular system for rapid whole genome alignment
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- License
- ART10
- Categories
- biology
- Package size
- 433.4 KiB, 1823.6 KiB installed
Description
MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/mummer | 4.0.1 |
| NetBSD | biology/mummer | 3.20nb10 |
| DragonFly | biology/mummer | 4.0.1 |
Install
Binary package:
pkg install mummerFrom the ports tree:
cd /usr/ports/biology/mummer/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= mummer>0:biology/mummer
LIB_DEPENDS= libumdmummer.so:biology/mummerPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 4.0.1 | 4.0.1 | 4.0.0.b2.2_3 | 4.0.1 | 4.0.1 |
| FreeBSD:14:quarterly | 4.0.1 | 4.0.1 | n/a | 4.0.1 | 4.0.1 |
| FreeBSD:15:latest | 4.0.1 | 4.0.1 | n/a | 4.0.1 | 4.0.1 |
| FreeBSD:15:quarterly | 4.0.1 | 4.0.1 | n/a | n/a | n/a |
| FreeBSD:16:latest | 4.0.1 | 4.0.1 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Build 1
yaggo: devel/yaggo
The full lists below include those, and their dependencies in turn.
Build dependencies 14
Run dependencies 1
Required by 1
Configuration
No options to configure.
- USES
- autoreconf compiler:c++17-lang gmake libtool perl5 shebangfix
- Service scripts
- none
Files
pkg-plist 65
- bin/combineMUMs
- bin/delta-filter
- bin/dnadiff
- bin/exact-tandems
- bin/mummer
- bin/mummer-annotate
- 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/mummer-4.0.1/include/compactsufsort/compactsufsort.hpp
- include/mummer-4.0.1/include/compactsufsort/compactsufsort_imp.hpp
- include/mummer-4.0.1/include/compactsufsort/const_iterator_traits.hpp
- include/mummer-4.0.1/include/compactsufsort/divsufsort_private.h
- include/mummer-4.0.1/include/compactsufsort/said_traits.hpp
- include/mummer-4.0.1/include/compactsufsort/sssort_imp.hpp
- include/mummer-4.0.1/include/compactsufsort/trsort_imp.hpp
- include/mummer-4.0.1/include/jellyfish/circular_buffer.hpp
- include/mummer-4.0.1/include/jellyfish/cooperative_pool2.hpp
- include/mummer-4.0.1/include/jellyfish/cpp_array.hpp
- include/mummer-4.0.1/include/jellyfish/divisor.hpp
- include/mummer-4.0.1/include/jellyfish/stream_manager.hpp
- include/mummer-4.0.1/include/jellyfish/whole_sequence_parser.hpp
- include/mummer-4.0.1/include/mt_skip_list/common.hpp
- include/mummer-4.0.1/include/mt_skip_list/set.hpp
- include/mummer-4.0.1/include/mummer/48bit_index.hpp
- include/mummer-4.0.1/include/mummer/48bit_iterator.hpp
- include/mummer-4.0.1/include/mummer/const_iterator_traits.hpp
- include/mummer-4.0.1/include/mummer/delta.hh
- include/mummer-4.0.1/include/mummer/dset.hpp
- include/mummer-4.0.1/include/mummer/fasta.hpp
- include/mummer-4.0.1/include/mummer/mgaps.hh
- include/mummer-4.0.1/include/mummer/nucmer.hpp
- include/mummer-4.0.1/include/mummer/openmp_qsort.hpp
- include/mummer-4.0.1/include/mummer/postnuc.hh
- include/mummer-4.0.1/include/mummer/redirect_to_pager.hpp
- include/mummer-4.0.1/include/mummer/sparseSA.hpp
- include/mummer-4.0.1/include/mummer/sparseSA_imp.hpp
- include/mummer-4.0.1/include/mummer/sw_align.hh
- include/mummer-4.0.1/include/mummer/sw_alignscore.hh
- include/mummer-4.0.1/include/mummer/tigrinc.hh
- include/mummer-4.0.1/include/mummer/timer.hpp
- include/mummer-4.0.1/include/mummer/translate.hh
- include/mummer-4.0.1/include/thread_pipe.hpp
- include/mummer-4.0.1/include/thread_pipe/circular_buffer.hpp
- include/mummer-4.0.1/include/thread_pipe/cooperative_pool2.hpp
- include/mummer-4.0.1/include/thread_pipe/divisor.hpp
- include/mummer-4.0.1/include/thread_pipe/traits.hpp
- lib/libumdmummer.so
- lib/libumdmummer.so.0
- lib/libumdmummer.so.0.0.0
- lib/mummer/Foundation.pm
- lib/mummer/tandem-repeat.awk
- libdata/pkgconfig/mummer.pc
- libexec/mummer/mgaps
- libexec/mummer/nucmer_ori
- libexec/mummer/postnuc
- libexec/mummer/postpro
- libexec/mummer/prenuc
- libexec/mummer/prepro
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| mummer4-mummer-v4.0.1_GH0.tar.gz | 1.839328e+07 | b866abcf75e0a24fbda8f8516defadfe523077d0d7303f941ff5d9673892eeab |
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