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Port details
mummer Modular system for rapid whole genome alignment
4.0.0.b2.2_1 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
4.0.0.b2.2Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2007-12-14 20:56:11
Last Update: 2018-12-12 01:35:36
SVN Revision: 487272
License: ART10
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.

WWW: http://mummer.sourceforge.net/
SVNWeb : Homepage
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (68 items)
  1. /usr/local/share/licenses/mummer-4.0.0.b2.2_1/catalog.mk
  2. /usr/local/share/licenses/mummer-4.0.0.b2.2_1/LICENSE
  3. /usr/local/share/licenses/mummer-4.0.0.b2.2_1/ART10
  4. bin/annotate
  5. bin/combineMUMs
  6. bin/delta-filter
  7. bin/dnadiff
  8. bin/exact-tandems
  9. bin/mummer
  10. bin/mummerplot
  11. bin/nucmer
  12. bin/promer
  13. bin/repeat-match
  14. bin/show-aligns
  15. bin/show-coords
  16. bin/show-diff
  17. bin/show-snps
  18. bin/show-tiling
  19. include/mummer-4.0.0beta2/include/compactsufsort/compactsufsort.hpp
  20. include/mummer-4.0.0beta2/include/compactsufsort/compactsufsort_imp.hpp
  21. include/mummer-4.0.0beta2/include/compactsufsort/const_iterator_traits.hpp
  22. include/mummer-4.0.0beta2/include/compactsufsort/divsufsort_private.h
  23. include/mummer-4.0.0beta2/include/compactsufsort/said_traits.hpp
  24. include/mummer-4.0.0beta2/include/compactsufsort/sssort_imp.hpp
  25. include/mummer-4.0.0beta2/include/compactsufsort/trsort_imp.hpp
  26. include/mummer-4.0.0beta2/include/jellyfish/circular_buffer.hpp
  27. include/mummer-4.0.0beta2/include/jellyfish/cooperative_pool2.hpp
  28. include/mummer-4.0.0beta2/include/jellyfish/cpp_array.hpp
  29. include/mummer-4.0.0beta2/include/jellyfish/divisor.hpp
  30. include/mummer-4.0.0beta2/include/jellyfish/stream_manager.hpp
  31. include/mummer-4.0.0beta2/include/jellyfish/whole_sequence_parser.hpp
  32. include/mummer-4.0.0beta2/include/mt_skip_list/common.hpp
  33. include/mummer-4.0.0beta2/include/mt_skip_list/set.hpp
  34. include/mummer-4.0.0beta2/include/mummer/48bit_index.hpp
  35. include/mummer-4.0.0beta2/include/mummer/48bit_iterator.hpp
  36. include/mummer-4.0.0beta2/include/mummer/const_iterator_traits.hpp
  37. include/mummer-4.0.0beta2/include/mummer/delta.hh
  38. include/mummer-4.0.0beta2/include/mummer/dset.hpp
  39. include/mummer-4.0.0beta2/include/mummer/fasta.hpp
  40. include/mummer-4.0.0beta2/include/mummer/mgaps.hh
  41. include/mummer-4.0.0beta2/include/mummer/nucmer.hpp
  42. include/mummer-4.0.0beta2/include/mummer/openmp_qsort.hpp
  43. include/mummer-4.0.0beta2/include/mummer/postnuc.hh
  44. include/mummer-4.0.0beta2/include/mummer/redirect_to_pager.hpp
  45. include/mummer-4.0.0beta2/include/mummer/sparseSA.hpp
  46. include/mummer-4.0.0beta2/include/mummer/sparseSA_imp.hpp
  47. include/mummer-4.0.0beta2/include/mummer/sw_align.hh
  48. include/mummer-4.0.0beta2/include/mummer/sw_alignscore.hh
  49. include/mummer-4.0.0beta2/include/mummer/tigrinc.hh
  50. include/mummer-4.0.0beta2/include/mummer/timer.hpp
  51. include/mummer-4.0.0beta2/include/mummer/translate.hh
  52. include/mummer-4.0.0beta2/include/thread_pipe.hpp
  53. include/mummer-4.0.0beta2/include/thread_pipe/circular_buffer.hpp
  54. include/mummer-4.0.0beta2/include/thread_pipe/cooperative_pool2.hpp
  55. include/mummer-4.0.0beta2/include/thread_pipe/divisor.hpp
  56. include/mummer-4.0.0beta2/include/thread_pipe/traits.hpp
  57. lib/libumdmummer.so
  58. lib/libumdmummer.so.0
  59. lib/libumdmummer.so.0.0.0
  60. lib/mummer/Foundation.pm
  61. lib/mummer/tandem-repeat.awk
  62. libdata/pkgconfig/mummer.pc
  63. libexec/mummer/mgaps
  64. libexec/mummer/postnuc
  65. libexec/mummer/postpro
  66. libexec/mummer/prepro
  67. @postexec /usr/sbin/service ldconfig restart > /dev/null
  68. @postunexec /usr/sbin/service ldconfig restart > /dev/null
  69. Collapse this list.
Dependency lines:
  • mummer>0:biology/mummer

To install the port: cd /usr/ports/biology/mummer/ && make install clean
To add the package: pkg install mummer

PKGNAME: mummer

There is no flavor information for this port.

distinfo:

TIMESTAMP = 1544513160
SHA256 (mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz) = 4b77fb57f0e7994ed0cb9886de23ce620b89cb16734df82ba492dbc750e387f1
SIZE (mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz) = 18369428


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. yaggo : devel/yaggo
  2. autoconf>=2.69 : devel/autoconf
  3. automake>=1.16.1 : devel/automake
  4. libtoolize : devel/libtool
  5. gmake : devel/gmake
  6. perl5>=5.26<5.27 : lang/perl5.26
Runtime dependencies:
  1. perl5>=5.26<5.27 : lang/perl5.26
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
autoreconf compiler:c++11-lang gmake libtool perl5 shebangfix

Master Sites:
  1. https://codeload.github.com/mummer4/mummer/tar.gz/v4.0.0beta2-2-g277dac5?dummy=/

Number of commits found: 23

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
12 Dec 2018 01:35:36
Original commit files touched by this commit  4.0.0.b2.2_1
Revision:487272
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
11 Dec 2018 07:48:12
Original commit files touched by this commit  4.0.0.b2.2
Revision:487223
yuri search for other commits by this committer
biology/mummer: Add USES=compiler:c++11-lang
11 Dec 2018 07:43:45
Original commit files touched by this commit  4.0.0.b2.2
Revision:487222
yuri search for other commits by this committer
biology/mummer: Update 3.23 -> 4.0.0beta2-2

Port changes:
* Moved to github
* It now installs itself
* It uses yaggo during build
11 Dec 2018 07:23:54
Original commit files touched by this commit  3.23_2
Revision:487221
yuri search for other commits by this committer
biology/mummer: Take maintainership
30 Oct 2017 02:27:23
Original commit files touched by this commit  3.23_2
Revision:453152
wen search for other commits by this committer
- Fix installing scripts and support binaries
- Add LICENSE

PR:		223098
Submitted by:	mzaki@niid.go.jp
05 Aug 2015 12:18:41
Original commit files touched by this commit  3.23_1
Revision:393581
amdmi3 search for other commits by this committer
Fix build on mips by properly respecting compiler and flags
20 Oct 2014 07:10:48
Original commit files touched by this commit  3.23_1
Revision:371237
bapt search for other commits by this committer
Cleanup plist
19 Jul 2014 22:00:17
Original commit files touched by this commit  3.23_1
Revision:362284
marino search for other commits by this committer
biology/mummer: Use OPSYS with OSVERSION

I don't think selecting clang as a function of OSVERSION is generally
desired, but if it's going to happen, make sure FreeBSD-specific
conditions are limited to FreeBSD by comparing OPSYS first.
27 Jun 2014 14:14:01
Original commit files touched by this commit  3.23_1
Revision:359532
miwi search for other commits by this committer
Fix compilation on 10+ (clang)
Fix format of WWW entry in pkg-descr

PR:		190798
11 Jun 2014 18:55:30
Original commit files touched by this commit  3.23
Revision:357526
marino search for other commits by this committer
Reset the 99 ports still listed under sylvio@

Sylvio's last commit was 17 months ago, a full 5 months after all of his
ports could have been reset per policy.  Given the push to complete
staging (48 ports are still unstaged, something like 70+ have already
been staged by other committers) and given that PRs are automatically
assigned but never addressed, it's better just to reset all the ports and
PRs so that it's clear to others that these ports are free to maintain.

Approved by:	portmgr (implicit)
09 Jun 2014 11:21:53
Original commit files touched by this commit  3.23
Revision:357139
olgeni search for other commits by this committer
Remove indefinite articles and trailing periods from COMMENT, plus
minor COMMENT typos and surrounding whitespace fixes. Categories A-C.

CR:		D196
Approved by:	portmgr (bapt)
01 Jun 2014 10:54:33
Original commit files touched by this commit  3.23
Revision:356093
ohauer search for other commits by this committer
- add stage support
13 Mar 2014 07:41:34
Original commit files touched by this commit  3.23
Revision:348042
miwi search for other commits by this committer
- Convert USE_GMAKE to USES
21 Feb 2014 13:35:26
Original commit files touched by this commit  3.23
Revision:345397
ehaupt search for other commits by this committer
Remove trailing whitespaces from category biology
10 Feb 2014 13:54:28
Original commit files touched by this commit  3.23
Revision:343634
ehaupt search for other commits by this committer
According to the Porter's Handbook (5.12.2.3.) default options must be added to
OPTIONS_DEFINE. This policy has been implemented only recently that's why we
have many ports violating this policy.

This patch adds the default options specified in the Porter's Handbook to
OPTIONS_DEFINE where they are being used. Ports maintained by
gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded.

Approved by:    portmgr (bapt)
03 Jan 2014 15:46:52
Original commit files touched by this commit  3.23
Revision:338550
adamw search for other commits by this committer
Convert biology to MDOCS and MEXAMPLES
20 Sep 2013 15:55:44
Original commit files touched by this commit  3.23
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
17 Jan 2012 00:51:39
Original commit files touched by this commit  3.23

sylvio search for other commits by this committer
- Update to 3.23
19 Mar 2011 12:38:54
Original commit files touched by this commit  3.22

miwi search for other commits by this committer
- Get Rid MD5 support
21 Mar 2010 17:18:20
Original commit files touched by this commit  3.22

sylvio search for other commits by this committer
- Update to 3.22

Approved by:    itetcu (mentor)
27 Nov 2009 22:52:30
Original commit files touched by this commit  3.21

sylvio search for other commits by this committer
- Update my mail address to FreeBSD

Approved by:    miwi (mentor)
28 Aug 2009 14:52:05
Original commit files touched by this commit  3.21

araujo search for other commits by this committer
- Update to 3.21.
- Reset maintainer to submitter.

PR:             ports/138192
Submitted by:   Sylvio Cesar <scjamorim@bsd.com.br>
14 Dec 2007 20:54:47
Original commit files touched by this commit  3.20

miwi search for other commits by this committer
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.

WWW:    http://mummer.sourceforge.net/

PR:             ports/118142
Submitted by:   Tony Maher

Number of commits found: 23

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