BSD Ports

biology/smithwaterman g20160702 FreeBSD

Smith-waterman-gotoh alignment algorithm

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
2414383046
License
GPLv2
Categories
biology
Package size
67.3 KiB, 328.8 KiB installed

Description

The Smith-Waterman algorithm performs local sequence alignment; that is, for determining similar regions between two strings of nucleic acid sequences or protein sequences. Instead of looking at the entire sequence, the Smith-Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure. Gotoh and Atschul added optimizations making it practical for larger problems.

In the other systems

SystemPortVersion
FreeBSDbiology/smithwatermang20160702
NetBSDwip/smithwaterman0.0.0.20160702
DragonFlybiology/smithwatermang20160702
HardenedBSDbiology/smithwatermang20160702
GhostBSDbiology/smithwatermang20160702

Install

Binary package:

pkg install smithwaterman

From the ports tree:

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

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

RUN_DEPENDS=	smithwaterman>0:biology/smithwaterman
LIB_DEPENDS=	libsw.so:biology/smithwaterman

Packages

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

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latestg20160702g20160702g20160702g20160702g20160702
FreeBSD:14:quarterlyg20160702g20160702n/ag20160702g20160702
FreeBSD:15:latestg20160702g20160702n/ag20160702g20160702
FreeBSD:15:quarterlyg20160702g20160702n/an/an/a
FreeBSD:16:latestg20160702g20160702n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

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

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

Build dependencies 3
Required by 1

Configuration

No options to configure.

USES
gmake
Service scripts
none

Files

pkg-plist 12
  • bin/smithwaterman
  • include/smithwaterman/BandedSmithWaterman.h
  • include/smithwaterman/IndelAllele.h
  • include/smithwaterman/LeftAlign.h
  • include/smithwaterman/Mosaik.h
  • include/smithwaterman/Repeats.h
  • include/smithwaterman/SmithWatermanGotoh.h
  • include/smithwaterman/convert.h
  • include/smithwaterman/disorder.h
  • lib/libsw.a
  • lib/libsw.so
  • lib/libsw.so.1
distinfo 1
FileSizeSHA256
ekg-smithwaterman-g20160702-2610e259611ae4cde8f03c72499d28f03f6d38a7_GH0.tar.gz391908e1b37ab0e8cd9d3d5cbfdba80258c0ebd0862749b531e213f44cdfe2fc541d8

Commit history 1

DateCommitCreditsLog message
2414383046 Jason W. Bacon Release numerous ports to ports@
I've been retired for a few years, and it is unlikely I will be doing any more scientific computing support in the future. I have continued to maintain ~160 ports to the best of my ability, mainly as a favor to the community, but I can no longer justify the time and effort required. I am therefore releasing most of my scientific ports, along with a few others, to ports@. I will continue to maintain ports I am actively using and those for which I am upstream.