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Port details
hmmer Profile hidden Markov models for biological sequence analysis
3.1b2 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
Maintainer: mzaki@niid.go.jp search for ports maintained by this maintainer
Port Added: unknown
License: GPLv3
HMMER is an implementation of profile hidden Markov model methods for
sensitive searches of biological sequence databases using multiple sequence
alignments as queries.

Given a multiple sequence alignment as input, HMMER builds a statistical
model called a "hidden Markov model" which can then be used as a query into
a sequence database to find (and/or align) additional homologues of the
sequence family.

WWW: http://hmmer.org/
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (73 items)
  1. /usr/local/share/licenses/hmmer-3.1b2/catalog.mk
  2. /usr/local/share/licenses/hmmer-3.1b2/LICENSE
  3. /usr/local/share/licenses/hmmer-3.1b2/GPLv3
  4. bin/alimask
  5. bin/hmmalign
  6. bin/hmmbuild
  7. bin/hmmc2
  8. bin/hmmconvert
  9. bin/hmmemit
  10. bin/hmmerfm-exactmatch
  11. bin/hmmfetch
  12. bin/hmmlogo
  13. bin/hmmpgmd
  14. bin/hmmpress
  15. bin/hmmscan
  16. bin/hmmsearch
  17. bin/hmmsim
  18. bin/hmmstat
  19. bin/jackhmmer
  20. bin/makehmmerdb
  21. bin/nhmmer
  22. bin/nhmmscan
  23. bin/phmmer
  24. include/cachedb.h
  25. include/hmmer.h
  26. include/impl_sse.h
  27. include/p7_config.h
  28. include/p7_gbands.h
  29. include/p7_gmxb.h
  30. include/p7_gmxchk.h
  31. include/p7_hmmcache.h
  32. lib/libhmmer.a
  33. man/man1/alimask.1.gz
  34. man/man1/hmmalign.1.gz
  35. man/man1/hmmbuild.1.gz
  36. man/man1/hmmconvert.1.gz
  37. man/man1/hmmemit.1.gz
  38. man/man1/hmmer.1.gz
  39. man/man1/hmmfetch.1.gz
  40. man/man1/hmmlogo.1.gz
  41. man/man1/hmmpgmd.1.gz
  42. man/man1/hmmpress.1.gz
  43. man/man1/hmmscan.1.gz
  44. man/man1/hmmsearch.1.gz
  45. man/man1/hmmsim.1.gz
  46. man/man1/hmmstat.1.gz
  47. man/man1/jackhmmer.1.gz
  48. man/man1/makehmmerdb.1.gz
  49. man/man1/nhmmer.1.gz
  50. man/man1/nhmmscan.1.gz
  51. man/man1/phmmer.1.gz
  52. share/doc/hmmer/COPYRIGHT
  53. share/doc/hmmer/Userguide.pdf
  54. share/examples/hmmer/7LESS_DROME
  55. share/examples/hmmer/HBB_HUMAN
  56. share/examples/hmmer/MADE1.hmm
  57. share/examples/hmmer/MADE1.out
  58. share/examples/hmmer/MADE1.sto
  59. share/examples/hmmer/Pkinase.hmm
  60. share/examples/hmmer/Pkinase.sto
  61. share/examples/hmmer/dna_target.fa
  62. share/examples/hmmer/fn3.hmm
  63. share/examples/hmmer/fn3.out
  64. share/examples/hmmer/fn3.sto
  65. share/examples/hmmer/globins4.hmm
  66. share/examples/hmmer/globins4.out
  67. share/examples/hmmer/globins4.sto
  68. share/examples/hmmer/globins45.fa
  69. share/examples/hmmer/minifam
  70. share/examples/hmmer/minifam.h3f
  71. share/examples/hmmer/minifam.h3i
  72. share/examples/hmmer/minifam.h3m
  73. share/examples/hmmer/minifam.h3p
  74. Collapse this list.

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

PKGNAME: hmmer

distinfo:

TIMESTAMP = 1510218548
SHA256 (hmmer-3.1b2.tar.gz) = dd16edf4385c1df072c9e2f58c16ee1872d855a018a2ee6894205277017b5536
SIZE (hmmer-3.1b2.tar.gz) = 5965253


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

Build dependencies:
  1. gmake : devel/gmake
There are no ports dependent upon this port

Configuration Options
===> The following configuration options are available for hmmer-3.1b2:
     DOCS=on: Build and/or install documentation
     EXAMPLES=on: Build and/or install examples
     TEST=off: Build and/or run tests
===> Use 'make config' to modify these settings

USES:
gmake

pkg-message:
---------------------------------------------------------------------------
HMMER reads three optional environment variables:
  HMMERDB  - directory location of HMM databases (e.g. PFAM)
  BLASTDB  - directory location of FASTA-formatted sequence databases
  BLASTMAT - directory location of PAM scoring matrices

The BLASTDB and BLASTMAT variables are shared with versions of BLAST such
as NCBI BLAST 2.0 (contained in the biology/ncbi-toolkit port).  If these
variables are set, you do not have to specify the full path to your
databases on the command line when using HMMER.

Please see the documentation for more information.
---------------------------------------------------------------------------

Master Sites:
  1. http://eddylab.org/software/hmmer3/3.1b2/

Number of commits found: 27

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
11 Nov 2017 12:51:52
Original commit files touched by this commit  3.1b2
Revision:453972
wen search for other commits by this committer
- Update to 3.1b2
- Pass maintainership to submitter

PR:		223561
Submitted by:	mzaki@niid.go.jp
Approved by:	bacon4000@gmail.com(previous maintainer)
13 Oct 2017 11:14:32
Original commit files touched by this commit  3.0_1
Revision:451981
bapt search for other commits by this committer
Remove dead master sites
25 Jun 2017 00:29:09
Original commit files touched by this commit  3.0_1
Revision:444251
linimon search for other commits by this committer
Begin deorbit burn of ia64.  We have not attempted to build packages for
it for many years.

While here, alphabetize ARCHs, pet portlint, and modernize usages.

Approved by:	portmgr (tier-2 blanket)
11 Dec 2015 08:48:57
Original commit files touched by this commit  3.0_1
Revision:403506
miwi search for other commits by this committer
- Update maintainer mail address
- Update/Remove MASTER_SITE

PR:		204755
Submitted by:	 jwbacon@tds.net (maintainer)
Approved by:	mat (mentor)
Differential Revision:	D4493
02 Apr 2015 15:41:32
Original commit files touched by this commit  3.0_1
Revision:383013
amdmi3 search for other commits by this committer
- Remove deprecated option
- Tweak compiler flags
- Add LICENSE
- Pass maintainership to submitter

PR:		199066
Submitted by:	jwbacon@tds.net
20 Oct 2014 07:10:48
Original commit files touched by this commit  3.0
Revision:371237
bapt search for other commits by this committer
Cleanup plist
15 Jul 2014 14:54:54
Original commit files touched by this commit  3.0
Revision:361934
adamw search for other commits by this committer
Add DOCS to OPTIONS_DEFINE to ports that check for PORT_OPTIONS:MDOCS.

While here, use OPTIONS helpers and re-enable manpage installation.
30 Dec 2013 18:08:15
Original commit files touched by this commit  3.0
Revision:338155
antoine search for other commits by this committer
Stage support
20 Sep 2013 15:55:44
Original commit files touched by this commit  3.0
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)
03 Aug 2013 08:45:52
Original commit files touched by this commit  3.0
Revision:324181
az search for other commits by this committer
- Convert to new perl framework
- Trim Makefile header
20 Jul 2013 15:08:45
Original commit files touched by this commit  3.0
Revision:323349
wen search for other commits by this committer
- Update to 3.0
- Convert to optionsNG
- Drop maintainership
01 Oct 2012 14:55:55
Original commit files touched by this commit  2.3.2
Revision:305131
wen search for other commits by this committer
- Take maintainership
01 Oct 2012 14:45:17
Original commit files touched by this commit  2.3.2
Revision:305130
tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
19 Mar 2011 12:38:54
Original commit files touched by this commit  2.3.2
miwi search for other commits by this committer
- Get Rid MD5 support
01 Feb 2009 08:17:14
Original commit files touched by this commit  2.3.2
pgollucci search for other commits by this committer
- Update download locations, update WWW

Reported by:    -fetch-original pointyhat run
22 Jan 2006 08:20:34
Original commit files touched by this commit  2.3.2
edwin search for other commits by this committer
SHA256ify

Approved by:    krion@
25 Nov 2004 22:58:29
Original commit files touched by this commit  2.3.2
sem search for other commits by this committer
- Remove a junk white space.
25 Nov 2004 22:35:52
Original commit files touched by this commit  2.3.2
sem search for other commits by this committer
- Update to 2.3.2
- Add WITH_PVM knob
- Pass maintainership to submitter

PR:             ports/74331
Submitted by:   Fernan Aguero <fernan(at)iib.unsam.edu.ar>
20 Nov 2004 08:09:49
Original commit files touched by this commit  2.2.g_1
linimon search for other commits by this committer
With portmgr hat on, reset inactive maintainer.  These ports are now up
for adoption.
31 Mar 2004 03:12:58
Original commit files touched by this commit  2.2.g_1
trevor search for other commits by this committer
SIZEify (maintainer timeout)
22 Oct 2003 09:29:55
Original commit files touched by this commit  2.2.g_1
osa search for other commits by this committer
Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.

Submitted by:   Oleg Karachevtsev <ok@etrust.ru>
A part of PR:   57992
07 Mar 2003 05:56:43
Original commit files touched by this commit  2.2.g_1
ade search for other commits by this committer
Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.
11 Jul 2002 10:52:14
Original commit files touched by this commit  2.2.g_1
wjv search for other commits by this committer
- Add patch that will, for -CURRENT only, change:  -pthread -> -lc_r
- Bump $PORTREVISION

Prompted by:    Various questions from Rune Linding <linding@EMBL-Heidelberg.DE>
22 Aug 2001 14:18:10
Original commit files touched by this commit
wjv search for other commits by this committer
- Update port to version 2.2g    
05 Jul 2001 09:58:12
Original commit files touched by this commit
wjv search for other commits by this committer
- General clean-up of port.   - Install PDF and HTML documentation.   - Take
over maintainership.    
04 Jul 2001 13:16:13
Original commit files touched by this commit
wjv search for other commits by this committer
- Add %%PORTDOCS%% support to pkg-plist.   - $INSTALL_MAN -> $INSTALL_DATA in
Makefile where appropriate.    
08 Oct 2000 00:23:30
Original commit files touched by this commit
asami search for other commits by this committer
Convert category biology to new layout.  

Number of commits found: 27

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