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Port details
hmmer Profile hidden Markov models for biological sequence analysis
3.3.2_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 View this port on Repology. pkg-fallout 3.3.2Version of this port present on the latest quarterly branch.
Maintainer: mzaki@e-mail.ne.jp search for ports maintained by this maintainer
Port Added: unknown
Last Update: 2024-02-22 13:23:46
Commit Hash: c080051
License: BSD3CLAUSE
WWW:
http://hmmer.org/
Description:
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (59 items)
Collapse this list.
  1. /usr/local/share/licenses/hmmer-3.3.2_1/catalog.mk
  2. /usr/local/share/licenses/hmmer-3.3.2_1/LICENSE
  3. /usr/local/share/licenses/hmmer-3.3.2_1/BSD3CLAUSE
  4. bin/alimask
  5. bin/hmmalign
  6. bin/hmmbuild
  7. bin/hmmconvert
  8. bin/hmmemit
  9. bin/hmmfetch
  10. bin/hmmlogo
  11. bin/hmmpgmd
  12. bin/hmmpgmd_shard
  13. bin/hmmpress
  14. bin/hmmscan
  15. bin/hmmsearch
  16. bin/hmmsim
  17. bin/hmmstat
  18. bin/jackhmmer
  19. bin/makehmmerdb
  20. bin/nhmmer
  21. bin/nhmmscan
  22. bin/phmmer
  23. share/man/man1/alimask.1.gz
  24. share/man/man1/hmmalign.1.gz
  25. share/man/man1/hmmbuild.1.gz
  26. share/man/man1/hmmc2.1.gz
  27. share/man/man1/hmmconvert.1.gz
  28. share/man/man1/hmmemit.1.gz
  29. share/man/man1/hmmer.1.gz
  30. share/man/man1/hmmfetch.1.gz
  31. share/man/man1/hmmlogo.1.gz
  32. share/man/man1/hmmpgmd.1.gz
  33. share/man/man1/hmmpgmd_shard.1.gz
  34. share/man/man1/hmmpress.1.gz
  35. share/man/man1/hmmscan.1.gz
  36. share/man/man1/hmmsearch.1.gz
  37. share/man/man1/hmmsim.1.gz
  38. share/man/man1/hmmstat.1.gz
  39. share/man/man1/jackhmmer.1.gz
  40. share/man/man1/makehmmerdb.1.gz
  41. share/man/man1/nhmmer.1.gz
  42. share/man/man1/nhmmscan.1.gz
  43. share/man/man1/phmmer.1.gz
  44. share/doc/hmmer/Userguide.pdf
  45. share/examples/hmmer/7LESS_DROME
  46. share/examples/hmmer/HBB_HUMAN
  47. share/examples/hmmer/MADE1.hmm
  48. share/examples/hmmer/MADE1.sto
  49. share/examples/hmmer/Pkinase.hmm
  50. share/examples/hmmer/Pkinase.sto
  51. share/examples/hmmer/dna_target.fa
  52. share/examples/hmmer/fn3.hmm
  53. share/examples/hmmer/fn3.sto
  54. share/examples/hmmer/globins4.hmm
  55. share/examples/hmmer/globins4.sto
  56. share/examples/hmmer/globins45.fa
  57. @owner
  58. @group
  59. @mode
Collapse this list.
Dependency lines:
  • hmmer>0:biology/hmmer
To install the port:
cd /usr/ports/biology/hmmer/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/hmmer
  • pkg install hmmer
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: hmmer
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: amd64 i386 powerpc powerpc64
distinfo:
TIMESTAMP = 1665491511 SHA256 (hmmer-3.3.2.tar.gz) = 92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69 SIZE (hmmer-3.3.2.tar.gz) = 18213049

Packages (timestamps in pop-ups are UTC):
hmmer
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest-3.3.2_1--3.3.2_1-3.3-
FreeBSD:13:quarterly-3.3.2_1--3.3.2_13.3.23.3.2-
FreeBSD:14:latest-3.3.2_1--3.3.2_13.3.2--
FreeBSD:14:quarterly-3.3.2_1--3.3.2_13.3.23.3.2-
FreeBSD:15:latest-3.3.2_1n/a-n/a3.3.23.3.2-
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
Test dependencies:
  1. python3.9 : lang/python39
  2. perl5>=5.36<5.37 : lang/perl5.36
This port is required by:
for Run
  1. biology/barrnap

Configuration Options:
===> The following configuration options are available for hmmer-3.3.2_1: 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
Options name:
biology_hmmer
USES:
compiler:c11 gmake perl5 python:test shebangfix
pkg-message:
For install:
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:
Expand this list (1 items)
Collapse this list.
  1. http://eddylab.org/software/hmmer/
Collapse this list.

Number of commits found: 44

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
3.3.2_1
22 Feb 2024 13:23:46
commit hash: c0800517ea855594a57280bc776d2185e84bcc20commit hash: c0800517ea855594a57280bc776d2185e84bcc20commit hash: c0800517ea855594a57280bc776d2185e84bcc20commit hash: c0800517ea855594a57280bc776d2185e84bcc20 files touched by this commit
Muhammad Moinur Rahman (bofh) search for other commits by this committer
biology/hmmer: Moved man to share/man

Approved by:    portmgr (blanket)
3.3.2
27 Jun 2023 19:34:34
commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb files touched by this commit
Rene Ladan (rene) search for other commits by this committer
all: remove explicit versions in USES=python for "3.x+"

The logic in USES=python will automatically convert this to 3.8+ by
itself.

Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.

finance/quickfix: mark BROKEN with PYTHON

libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp  -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
          ^~~~~~~~~~
1 warning and 1 error generated.

Reviewed by:	portmgr, vishwin, yuri
Differential Revision:	<https://reviews.freebsd.org/D40568>
3.3.2
11 Oct 2022 20:13:01
commit hash: b532c5dd966eb638a5616fc7819657f007c08848commit hash: b532c5dd966eb638a5616fc7819657f007c08848commit hash: b532c5dd966eb638a5616fc7819657f007c08848commit hash: b532c5dd966eb638a5616fc7819657f007c08848 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/hmmer: Update to 3.3.2

No release notes.  See commits for changes:
https://github.com/EddyRivasLab/hmmer

PR:             266968
Reported by:    mzaki@e-mail.ne.jp
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
3.3
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
3.3
20 Jul 2022 14:20:57
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
(Only the first 15 lines of the commit message are shown above View all of this commit message)
3.3
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
3.3
10 Mar 2021 16:09:46
Revision:568013Original commit files touched by this commit
pkubaj search for other commits by this committer
biology/hmmer: disable on powerpc64le and powerpcspe

Altivec/VSX code in this port works only on big-endian POWER.
powerpcspe has neither SSE2 nor Altivec.
3.3
24 Sep 2020 20:29:35
Revision:549947Original commit files touched by this commit
linimon search for other commits by this committer
Also enable on powerpc64le.

Approved by:	portmgr (tier-2 blanket)
3.3
29 Jan 2020 05:55:12
Revision:524533Original commit files touched by this commit
fernape search for other commits by this committer
biology/hmmer: update to 3.3

PR:	243244
Submitted by:	mzaki@e-mail.ne.jp (maintainer)
3.2.1_1
13 Aug 2019 16:00:39
Revision:508834Original commit files touched by this commit
mat search for other commits by this committer
Convert to UCL & cleanup pkg-message (categories a-c)
3.2.1_1
26 Jul 2019 20:46:57
Revision:507372Original commit files touched by this commit
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

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, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
3.2.1
18 Feb 2019 01:30:24
Revision:493230Original commit files touched by this commit
linimon search for other commits by this committer
vec_splats function is not supported by base GCC.  Add USES=compiler:c11
to fix build on powerpc platforms.

PR:		235514
Submitted by:	Piotr Kubaj
Approved by:	portmgr (tier-2 blanket)
3.2.1
11 Jul 2018 15:15:04
Revision:474455Original commit files touched by this commit
swills search for other commits by this committer
biology/hmmer: update to 3.2.1

PR:		229693
Submitted by:	Motomichi Matsuzaki <mzaki@niid.go.jp> (maintainer)
3.1b2
18 Dec 2017 04:28:28
Revision:456588Original commit files touched by this commit
linimon search for other commits by this committer
Back out previous commits by jbeich demand.
3.1b2
18 Dec 2017 02:41:24
Revision:456579Original commit files touched by this commit
linimon search for other commits by this committer
Bah.  Remove spare line from cut-and-paste.
3.1b2
18 Dec 2017 02:32:47
Revision:456578Original commit files touched by this commit
linimon search for other commits by this committer
Attempt to fix build on non-x86 archs.  Untested, but does no harm
on x86.

Approved by:	portmgr (tier-2 blanket)
3.1b2
11 Nov 2017 12:51:52
Revision:453972Original commit files touched by this commit
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)
3.0_1
13 Oct 2017 11:14:32
Revision:451981Original commit files touched by this commit
bapt search for other commits by this committer
Remove dead master sites
3.0_1
25 Jun 2017 00:29:09
Revision:444251Original commit files touched by this commit
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)
3.0_1
11 Dec 2015 08:48:57
Revision:403506Original commit files touched by this commit
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
3.0_1
02 Apr 2015 15:41:32
Revision:383013Original commit files touched by this commit
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
3.0
20 Oct 2014 07:10:48
Revision:371237Original commit files touched by this commit
bapt search for other commits by this committer
Cleanup plist
3.0
15 Jul 2014 14:54:54
Revision:361934Original commit files touched by this commit
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.
3.0
30 Dec 2013 18:08:15
Revision:338155Original commit files touched by this commit
antoine search for other commits by this committer
Stage support
3.0
20 Sep 2013 15:55:44
Revision:327709Original commit files touched by this commit
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
3.0
03 Aug 2013 08:45:52
Revision:324181Original commit files touched by this commit
az search for other commits by this committer
- Convert to new perl framework
- Trim Makefile header
3.0
20 Jul 2013 15:08:45
Revision:323349Original commit files touched by this commit
wen search for other commits by this committer
- Update to 3.0
- Convert to optionsNG
- Drop maintainership
2.3.2
01 Oct 2012 14:55:55
Revision:305131Original commit files touched by this commit
wen search for other commits by this committer
- Take maintainership
2.3.2
01 Oct 2012 14:45:17
Revision:305130Original commit files touched by this commit
tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
2.3.2
19 Mar 2011 12:38:54
Original commit files touched by this commit
miwi search for other commits by this committer
- Get Rid MD5 support
2.3.2
01 Feb 2009 08:17:14
Original commit files touched by this commit
pgollucci search for other commits by this committer
- Update download locations, update WWW

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

Approved by:    krion@
2.3.2
25 Nov 2004 22:58:29
Original commit files touched by this commit
sem search for other commits by this committer
- Remove a junk white space.
2.3.2
25 Nov 2004 22:35:52
Original commit files touched by this commit
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>
2.2.g_1
20 Nov 2004 08:09:49
Original commit files touched by this commit
linimon search for other commits by this committer
With portmgr hat on, reset inactive maintainer.  These ports are now up
for adoption.
2.2.g_1
31 Mar 2004 03:12:58
Original commit files touched by this commit
trevor search for other commits by this committer
SIZEify (maintainer timeout)
2.2.g_1
22 Oct 2003 09:29:55
Original commit files touched by this commit
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
2.2.g_1
07 Mar 2003 05:56:43
Original commit files touched by this commit
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.
2.2.g_1
11 Jul 2002 10:52:14
Original commit files touched by this commit
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
commit hash: fp1.17631@dev.null.freshports.orgcommit hash: fp1.17631@dev.null.freshports.orgcommit hash: fp1.17631@dev.null.freshports.orgcommit hash: fp1.17631@dev.null.freshports.org 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
commit hash: fp1.15827@dev.null.freshports.orgcommit hash: fp1.15827@dev.null.freshports.orgcommit hash: fp1.15827@dev.null.freshports.orgcommit hash: fp1.15827@dev.null.freshports.org 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
commit hash: fp1.15794@dev.null.freshports.orgcommit hash: fp1.15794@dev.null.freshports.orgcommit hash: fp1.15794@dev.null.freshports.orgcommit hash: fp1.15794@dev.null.freshports.org 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
commit hash: fp1.4706@dev.null.freshports.orgcommit hash: fp1.4706@dev.null.freshports.orgcommit hash: fp1.4706@dev.null.freshports.orgcommit hash: fp1.4706@dev.null.freshports.org files touched by this commit
asami search for other commits by this committer
Convert category biology to new layout.  

Number of commits found: 44