biology/wise 2.4.1_1

Intelligent algorithms for DNA searches

Repository: FreeBSD ports
Maintainer: [email protected]
License: BSD3CLAUSE, GPLv2
Categories: biology
Package size: 1327.5 KiB, 10994.0 KiB installed

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)

Install

As a binary package — by origin, or by package name:

pkg install biology/wise
pkg install wise

From the ports tree:

cd /usr/ports/biology/wise/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	wise>0:biology/wise

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repository	aarch64	amd64	armv6	armv7	i386
FreeBSD:14:latest	2.4.1_1	2.4.1_1	2.4.1_1	2.4.1_1	2.4.1_1
FreeBSD:14:quarterly	2.4.1_1	2.4.1_1	n/a	2.4.1_1	2.4.1_1
FreeBSD:15:latest	2.4.1_1	2.4.1_1	n/a	2.4.1_1	2.4.1_1
FreeBSD:15:quarterly	2.4.1_1	2.4.1_1	n/a	n/a	n/a
FreeBSD:16:latest	2.4.1_1	2.4.1_1	n/a	n/a	n/a
FreeBSD:16:quarterly	n/a	n/a	n/a	n/a	n/a

Repository

aarch64

amd64

armv6

armv7

i386

FreeBSD:14:latest

2.4.1_1

FreeBSD:14:quarterly

2.4.1_1

n/a

2.4.1_1

FreeBSD:15:latest

2.4.1_1

n/a

2.4.1_1

FreeBSD:15:quarterly

2.4.1_1

n/a

FreeBSD:16:latest

2.4.1_1

n/a

FreeBSD:16:quarterly

n/a

Dependencies

The Makefile names none itself; they come from USES and USE_*.

The full lists below include those, and their dependencies in turn.

All build dependencies 16

All run dependencies 15

No port depends on this one.

Configuration

Options name: biology_wise

Option	Default	Description
DOCS	off	Build and/or install documentation
EXAMPLES	off	Build and/or install examples

Option

Default

Description

DOCS

off

Build and/or install documentation

EXAMPLES

off

Build and/or install examples

USES: gnome pkgconfig
Service scripts: none

Message after installing

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

===>   NOTICE:

The wise port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing

Files

distinfo 1

File	Size	SHA256
wise2.4.1.tar.gz	3.19391e+06	240e2b12d6cd899040e2efbcb85b0d3c10245c255f3d07c1db45d0af5a4d5fa1

File

Size

SHA256

wise2.4.1.tar.gz

3.19391e+06

240e2b12d6cd899040e2efbcb85b0d3c10245c255f3d07c1db45d0af5a4d5fa1

Master sites 1

http://www.ebi.ac.uk/~birney/wise2/

Commit history 0

No commits in the history this site was built from.