"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)
===> 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
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
all: drop support for expired FreeBSD 14.0
Simplify expressions for FreeBSD 13.X
Reviewed by: many
Differential Revision: https://reviews.freebsd.org/D46601
*/*: 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
*/*: 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)
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)
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 )
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 )
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.
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>
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>
