BSD Ports

biology/fasta 21.1.1_1 FreeBSD

Collection of programs for searching DNA and protein databases

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
License
FASTA
Categories
biology
Package size
112.0 KiB, 480.3 KiB installed

Description

Version 2 of the FASTA packages contains many programs for performing sequence comparisons, producing local alignments, and other related tasks for analysing DNA and proteins.

Currently, the FASTA2 suite is in maintenance mode. This package provides the analysis tools from FASTA2. The searching programs are available in version 3 of the FASTA packages, which may be found in the port biology/fasta3.

FASTA is described in: W. R. Pearson and D. J. Lipman (1988), "Improved Tools for Biological Sequence Analysis", PNAS 85:2444- 2448, and W. R. Pearson (1990) "Rapid and Sensitive Sequence Comparison with FASTP and FASTA" Methods in Enzymology 183:63- 98).

The FASTA2 suite is distributed freely subject to the condition that it may not be sold or incorporated into a commercial product.

In the other systems

SystemPortVersion
FreeBSDbiology/fasta21.1.1_1
NetBSDwip/fasta36.3.5.4
DragonFlybiology/fasta21.1.1_1
HardenedBSDbiology/fasta21.1.1_1
GhostBSDbiology/fasta21.1.1_1

Install

Binary package:

pkg install fasta

From the ports tree:

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

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

RUN_DEPENDS=	fasta>0:biology/fasta

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:latest21.1.1_121.1.1_121.1.121.1.1_121.1.1_1
FreeBSD:14:quarterly21.1.1_121.1.1_1n/a21.1.1_121.1.1_1
FreeBSD:15:latest21.1.1_121.1.1_1n/a21.1.1_121.1.1_1
FreeBSD:15:quarterly21.1.1_121.1.1_1n/an/an/a
FreeBSD:16:latest21.1.1_121.1.1_1n/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.

No port depends on this one.

Configuration

Options name: biology_fasta

OptionDefaultDescription
DOCSoffBuild and/or install documentation
Service scripts
none
Conflicts with
align

Message after installing

The FASTA3 package has been successfully installed.

NB:  A sample configuration file has been installed to /usr/local/etc as
"fastlibs.sample".  This may be renamed to "fastlibs" and edited
to suit the requirements of a particular site.

In order to use the FASTA3 programs, a user must set the environment
variable FASTLIBS to contain the full path of the FASTA3 configuration
file, e.g.:

- set FASTLIBS to:  "/usr/local/etc/fastlibs"

===>   NOTICE:

The fasta 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

Manual pages 14
  • align(1)
  • align0(1)
  • fasta(1)
  • fastx(1)
  • lalign(1)
  • lfasta(1)
  • plalign(1)
  • plfasta(1)
  • prdf(1)
  • prss(1)
  • randseq(1)
  • ssearch(1)
  • tfasta(1)
  • tfastx(1)
pkg-plist 21
  • bin/align
  • bin/align0
  • bin/chofas
  • bin/garnier
  • bin/lalign
  • bin/plalign
  • bin/psgrease
  • share/man/man1/align.1.gz
  • share/man/man1/align0.1.gz
  • share/man/man1/fasta.1.gz
  • share/man/man1/fastx.1.gz
  • share/man/man1/lalign.1.gz
  • share/man/man1/lfasta.1.gz
  • share/man/man1/plalign.1.gz
  • share/man/man1/plfasta.1.gz
  • share/man/man1/prdf.1.gz
  • share/man/man1/prss.1.gz
  • share/man/man1/randseq.1.gz
  • share/man/man1/ssearch.1.gz
  • share/man/man1/tfasta.1.gz
  • share/man/man1/tfastx.1.gz
distinfo 1
FileSizeSHA256
fasta-21.1.1.shar.Z461511553da3c5ef3a9e9e37784c2dcd77982b664f501e10b57ab8c4dcfe99c5039c82
Master sites 2
  • http://faculty.virginia.edu/wrpearson/fasta/fasta2/
  • ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/fasta2/

Commit history 0

No commits in the history this site was built from.