notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Want a good monitor light? See my photosAll times are UTC
Ukraine
This referral link gives you 10% off a Fastmail.com account and gives me a discount on my Fastmail account.

Get notified when packages are built

A new feature has been added. FreshPorts already tracks package built by the FreeBSD project. This information is displayed on each port page. You can now get an email when FreshPorts notices a new package is available for something on one of your watch lists. However, you must opt into that. Click on Report Subscriptions on the right, and New Package Notification box, and click on Update.

Finally, under Watch Lists, click on ABI Package Subscriptions to select your ABI (e.g. FreeBSD:14:amd64) & package set (latest/quarterly) combination for a given watch list. This is what FreshPorts will look for.

Port details
wise Intelligent algorithms for DNA searches
2.4.1_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 2.4.1_1Version of this port present on the latest quarterly branch.
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: 2002-09-10 13:59:05
Last Update: 2023-07-26 00:48:20
Commit Hash: 95274bf
License: BSD3CLAUSE GPLv2
WWW:
http://www.ebi.ac.uk/Wise2/
Description:
"Wise2 is package that is focused on comparing DNA sequences at the level of its conceptual translation, regardless of sequencing error and introns. This really is a rewrite of the old wisetools package, which I wrote about 3 years ago. It can compare a single protein or a profile HMM to a genomic DNA sequence, and predict a gene structure. This is algorithm, called genewise, is one of the algorithms available in Wise2. There are other algorithms focused on EST data rather than genomic data, as well as some other algorithm curios." - from the web site (Ewan Birney)
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (39 items)
Collapse this list.
  1. bin/dba
  2. bin/dnal
  3. bin/estwise
  4. bin/estwisedb
  5. bin/genewise
  6. bin/genewisedb
  7. bin/promoterwise
  8. bin/psw
  9. bin/pswdb
  10. bin/scanwise
  11. bin/scanwise_server
  12. share/wise/BLOSUM30.bla
  13. share/wise/BLOSUM45.bla
  14. share/wise/BLOSUM62.bla
  15. share/wise/BLOSUM80.bla
  16. share/wise/aa.rnd
  17. share/wise/cb.tmf
  18. share/wise/codon.table
  19. share/wise/gene.stat
  20. share/wise/gon120.bla
  21. share/wise/gon160.bla
  22. share/wise/gon200.bla
  23. share/wise/gon250.bla
  24. share/wise/gon350.bla
  25. share/wise/human.gf
  26. share/wise/human.gp
  27. share/wise/human.stats
  28. share/wise/idenity.bla
  29. share/wise/methods
  30. share/wise/pb.gf
  31. share/wise/pombe.gf
  32. share/wise/tm.pri
  33. share/wise/wise.2
  34. share/wise/wise.per
  35. share/wise/worm.gf
  36. /usr/local/share/licenses/wise-2.4.1_1/catalog.mk
  37. /usr/local/share/licenses/wise-2.4.1_1/LICENSE
  38. /usr/local/share/licenses/wise-2.4.1_1/BSD3CLAUSE
  39. /usr/local/share/licenses/wise-2.4.1_1/GPLv2
Collapse this list.
Dependency lines:
  • wise>0:biology/wise
To install the port:
cd /usr/ports/biology/wise/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/wise
  • pkg install wise
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: wise
Flavors: there is no flavor information for this port.
distinfo:
SHA256 (wise2.4.1.tar.gz) = 240e2b12d6cd899040e2efbcb85b0d3c10245c255f3d07c1db45d0af5a4d5fa1 SIZE (wise2.4.1.tar.gz) = 3193910

Packages (timestamps in pop-ups are UTC):
wise
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.4.1_12.4.1_12.4.1_12.4.1_12.4.1_1---
FreeBSD:13:quarterly2.4.1_12.4.1_1-2.4.1_12.4.1_12.4.1_12.4.1_12.4.1_1
FreeBSD:14:latest2.4.1_12.4.1_12.4.1_12.4.1_12.4.1_12.4.1_1-2.4.1_1
FreeBSD:14:quarterly2.4.1_12.4.1_1-2.4.1_12.4.1_12.4.1_12.4.1_12.4.1_1
FreeBSD:15:latest2.4.1_12.4.1_1n/a2.4.1_1n/a2.4.1_12.4.1_12.4.1_1
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. pkgconf>=1.3.0_1 : devel/pkgconf
Library dependencies:
  1. libglib-2.0.so : devel/glib20
  2. libintl.so : devel/gettext-runtime
There are no ports dependent upon this port

Configuration Options:
===> The following configuration options are available for wise-2.4.1_1: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings
Options name:
biology_wise
USES:
gnome pkgconfig
pkg-message:
For install:
Welcome to Wise2.2 You must set your WISECONFIGDIR to the config directory before using the programs: in (t)csh: setenv WISECONFIGDIR /usr/local/share/wise/ in (ba)sh: export WISECONFIGDIR=/usr/local/share/wise/ To try an example: cd /usr/local/share/examples/wise genewise road.pep human.genomic
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. http://www.ebi.ac.uk/~birney/wise2/
Collapse this list.

Number of commits found: 35

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.4.1_1
26 Jul 2023 00:48:20
commit hash: 95274bf4f99c71fc056013d966aec239161dfd74commit hash: 95274bf4f99c71fc056013d966aec239161dfd74commit hash: 95274bf4f99c71fc056013d966aec239161dfd74commit hash: 95274bf4f99c71fc056013d966aec239161dfd74 files touched by this commit
Muhammad Moinur Rahman (bofh) search for other commits by this committer
*/*: Fix build with llvm16 on 13.2-STABLE

As like as HEAD(14.0-RELEASE) llvm16 was merged in base for 13.2-STABLE
with the OSVERSION 1302507.

- Utilize USE_CXXSTD=c++14 or similar solution where applicable
- Update conditionals to addtionally check for OSVERSION greater than
  1302507 and less than 1400000

Approved by:	portmgr (blanket)
Sponsored by:	The FreeBSD Foundation
2.4.1_1
21 Jul 2023 19:57:53
commit hash: 1f42cbbadb84f0f50087d28aa8a349bcab2760dfcommit hash: 1f42cbbadb84f0f50087d28aa8a349bcab2760dfcommit hash: 1f42cbbadb84f0f50087d28aa8a349bcab2760dfcommit hash: 1f42cbbadb84f0f50087d28aa8a349bcab2760df files touched by this commit
Muhammad Moinur Rahman (bofh) search for other commits by this committer
biology/wise: Fix build with llvm16

Sponsored by:	The FreeBSD Foundation
2.4.1_1
17 May 2023 16:30:15
commit hash: 9b178ffd7e2fd77fecb8c80d22f7c80bc9e93977commit hash: 9b178ffd7e2fd77fecb8c80d22f7c80bc9e93977commit hash: 9b178ffd7e2fd77fecb8c80d22f7c80bc9e93977commit hash: 9b178ffd7e2fd77fecb8c80d22f7c80bc9e93977 files touched by this commit
Muhammad Moinur Rahman (bofh) search for other commits by this committer
*/*: llvm15 build fixes

llvm15 was also merged into 13.2-STABLE effective from OSVERSION
1302505. Fix the ports that failed to build with llvm15.

Approved by:	portmgr (blanket)
2.4.1_1
14 May 2023 19:59:10
commit hash: 85200081ed9b01eefc54b77f0863e1825ce9b6abcommit hash: 85200081ed9b01eefc54b77f0863e1825ce9b6abcommit hash: 85200081ed9b01eefc54b77f0863e1825ce9b6abcommit hash: 85200081ed9b01eefc54b77f0863e1825ce9b6ab files touched by this commit
Muhammad Moinur Rahman (bofh) search for other commits by this committer
biology/wise: Unbreak on HEAD

- Add LICENSE BSD3CLAUSE GPLv2
- Pet portclippy
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)
2.4.1_1
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)
2.4.1_1
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)
2.4.1_1
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.
2.4.1_1
08 Nov 2019 09:27:57
Revision:517040Original commit files touched by this commit
tobik search for other commits by this committer
a-b: Add missing USES={gnome,php,sdl,xorg}
2.4.1_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)
2.4.1_1
08 Dec 2016 19:52:20
Revision:428152Original commit files touched by this commit
tijl search for other commits by this committer
Remove libintl.so.9 compatibility link that was added in r374303 to
prevent massive PORTREVISION bumps.  Bump dependent ports that have not
been bumped since.
2.4.1
21 Jun 2016 09:05:06
Revision:417195Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Switch to options helpers
- Regenerate patches with `make makepatch`
2.4.1
13 May 2016 18:39:07
Revision:415129Original commit files touched by this commit
bapt search for other commits by this committer
Prevent collision with getline(3)
2.4.1
20 Dec 2014 17:27:09
Revision:375014Original commit files touched by this commit
bapt search for other commits by this committer
Cleanup plist
2.4.1
24 Mar 2014 10:46:35
Revision:348933Original commit files touched by this commit
pawel search for other commits by this committer
- Add staging support
- Unmute install commands
2.4.1
05 Feb 2014 23:42:06
Revision:342903Original commit files touched by this commit
marino search for other commits by this committer
biology/wise: Add dragonfly support
2.4.1
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)
2.4.1
03 Aug 2013 13:44:01
Revision:324191Original commit files touched by this commit Sanity Test Failure
mat search for other commits by this committer
- Convert to new perl framework
- Remove MAKE_JOBS_SAFE=yes, it's the default.
2.4.1
03 May 2013 20:48:35
Revision:317247Original commit files touched by this commit
bapt search for other commits by this committer
Fix build by adding an explicit dep on pkgconf
2.4.1
02 Mar 2013 14:50:25
Revision:313250Original commit files touched by this commit
miwi search for other commits by this committer
- Update to 2.4.1

PR:		176552
Submitted by:	Ports Fury
2.2.0
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
2.2.0
16 Nov 2010 23:55:41
Original commit files touched by this commit
skreuzer search for other commits by this committer
Fix plist.

Reported by:    QAT
2.2.0
08 Jan 2010 01:30:20
Original commit files touched by this commit
pgollucci search for other commits by this committer
- SBU_FILES += pkg-message

PR:             ports/142409
Submitted by:   Sevan Janiyan <venture37@geeklan.co.uk>
2.2.0
26 Dec 2006 12:46:34
Original commit files touched by this commit
linimon search for other commits by this committer
Reset tonymaher@optusnet.com.au due to maintainer-timeouts and no response
to email.

Hat:            portmgr
2.2.0
03 May 2006 23:26:35
Original commit files touched by this commit
edwin search for other commits by this committer
Remove USE_REINPLACE from all categories starting with B
2.2.0
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@
2.2.0
09 Jan 2006 03:25:03
Original commit files touched by this commit
edwin search for other commits by this committer
Fix maintainer address

    From: Tony Maher <anthony.maher@uts.edu.au>
    To: Edwin Groothuis <edwin@FreeBSD.org>
    Subject: Re: ports/91537: maths/xgobi - download site moved/maintainer
addressupdate

    Actually I need  modify all my ports to use OptusNet rather than
    Biolateral.  Is there an easy way to do this or should I submit a
    separate 1-line patch and PR for each port?

    biology/crimap
    biology/dna-qc
    biology/flip
    biology/primer3
    biology/seqio
    biology/wise
    math/xgobi
    net/generic-nqs

Submitted by:   Tony Maher <anthony.maher@uts.edu.au>
2.2.0
31 Mar 2004 03:12:58
Original commit files touched by this commit
trevor search for other commits by this committer
SIZEify (maintainer timeout)
2.2.0
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
2.2.0
24 Sep 2003 11:32:44
Original commit files touched by this commit
edwin search for other commits by this committer
Port update (maintainer): biology/wise

        Fenner's porsurvey show wise no longer available at original
        site.  Original site readme shows it has moved so update
        the MASTER_SITES accordingly.

PR:             ports/57154
Submmited by:   Tony Maher <tonymaher@optushome.com.au>
2.2.0
21 Feb 2003 11:01:38
Original commit files touched by this commit
knu search for other commits by this committer
De-pkg-comment.
2.2.0
14 Jan 2003 05:30:42
Original commit files touched by this commit
kris search for other commits by this committer
Add missing file
2.2.0
05 Nov 2002 01:44:12
Original commit files touched by this commit
edwin search for other commits by this committer
Modify replace RE to match syntax of sed now ("\)" -> ")"
Noticed by: bento
2.2.0
04 Nov 2002 05:46:38
Original commit files touched by this commit
edwin search for other commits by this committer
PERL -> REINPLACE
And some ports have USE_PERL5=yes now.
2.2.0
10 Sep 2002 13:58:40
Original commit files touched by this commit
dinoex search for other commits by this committer
"Wise2 is package that is focused on comparing DNA sequences at
the level of its conceptual translation, regardless of sequencing
error and introns."

Number of commits found: 35