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Port details
mummer Modular system for rapid whole genome alignment
3.23_2 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

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 14 Dec 2007 20:56:11
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 : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (34 items)
  1. /usr/local/share/licenses/mummer-3.23_2/catalog.mk
  2. /usr/local/share/licenses/mummer-3.23_2/LICENSE
  3. /usr/local/share/licenses/mummer-3.23_2/ART10
  4. bin/annotate
  5. bin/combineMUMs
  6. bin/delta-filter
  7. bin/dnadiff
  8. bin/exact-tandems
  9. bin/gaps
  10. bin/mapview
  11. bin/mgaps
  12. bin/mummer
  13. bin/mummerplot
  14. bin/nucmer
  15. bin/nucmer2xfig
  16. bin/promer
  17. bin/repeat-match
  18. bin/run-mummer1
  19. bin/run-mummer3
  20. bin/show-aligns
  21. bin/show-coords
  22. bin/show-diff
  23. bin/show-snps
  24. bin/show-tiling
  25. libexec/mummer/Foundation.pm
  26. libexec/mummer/postnuc
  27. libexec/mummer/postpro
  28. libexec/mummer/prenuc
  29. libexec/mummer/prepro
  30. libexec/mummer/tandem-repeat.awk
  31. share/doc/mummer/COPYRIGHT
  32. share/doc/mummer/INSTALL
  33. share/doc/mummer/LICENSE
  34. share/doc/mummer/README
  35. Collapse this list.

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

PKGNAME: mummer

distinfo:

TIMESTAMP = 1509357521
SHA256 (MUMmer3.23.tar.gz) = 1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f
SIZE (MUMmer3.23.tar.gz) = 3160143


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

Build dependencies:
  1. gmake : devel/gmake
  2. perl5>=5.24<5.25 : lang/perl5.24
Runtime dependencies:
  1. perl5>=5.24<5.25 : lang/perl5.24
There are no ports dependent upon this port

Configuration Options
===> The following configuration options are available for mummer-3.23_2:
     DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings

USES:
gmake perl5 shebangfix

Master Sites:
  1. http://cytranet.dl.sourceforge.net/project/mummer/mummer/3.23/
  2. http://downloads.sourceforge.net/project/mummer/mummer/3.23/
  3. http://excellmedia.dl.sourceforge.net/project/mummer/mummer/3.23/
  4. http://freefr.dl.sourceforge.net/project/mummer/mummer/3.23/
  5. http://jaist.dl.sourceforge.net/project/mummer/mummer/3.23/
  6. http://kent.dl.sourceforge.net/project/mummer/mummer/3.23/
  7. http://nchc.dl.sourceforge.net/project/mummer/mummer/3.23/
  8. http://netcologne.dl.sourceforge.net/project/mummer/mummer/3.23/
  9. http://netix.dl.sourceforge.net/project/mummer/mummer/3.23/
  10. http://superb-dca2.dl.sourceforge.net/project/mummer/mummer/3.23/
  11. http://superb-sea2.dl.sourceforge.net/project/mummer/mummer/3.23/
  12. http://ufpr.dl.sourceforge.net/project/mummer/mummer/3.23/
  13. http://vorboss.dl.sourceforge.net/project/mummer/mummer/3.23/
  14. https://cytranet.dl.sourceforge.net/project/mummer/mummer/3.23/
  15. https://downloads.sourceforge.net/project/mummer/mummer/3.23/
  16. https://excellmedia.dl.sourceforge.net/project/mummer/mummer/3.23/
  17. https://freefr.dl.sourceforge.net/project/mummer/mummer/3.23/
  18. https://jaist.dl.sourceforge.net/project/mummer/mummer/3.23/
  19. https://kent.dl.sourceforge.net/project/mummer/mummer/3.23/
  20. https://nchc.dl.sourceforge.net/project/mummer/mummer/3.23/
  21. https://netcologne.dl.sourceforge.net/project/mummer/mummer/3.23/
  22. https://netix.dl.sourceforge.net/project/mummer/mummer/3.23/
  23. https://superb-dca2.dl.sourceforge.net/project/mummer/mummer/3.23/
  24. https://superb-sea2.dl.sourceforge.net/project/mummer/mummer/3.23/
  25. https://ufpr.dl.sourceforge.net/project/mummer/mummer/3.23/
  26. https://vorboss.dl.sourceforge.net/project/mummer/mummer/3.23/

Number of commits found: 19

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
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: 19

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