biology/emboss 6.6.0_7

Collection of open source tools for genetic sequence analysis

Repository: FreeBSD ports
Maintainer: [email protected]
License: GPLv2
Categories: biology
Package size: 79979.9 KiB, 512996.7 KiB installed

Description

The European Molecular Biology Open Software Suite (EMBOSS) is a comprehensive set (about 100) of open source tools for genetic sequence analysis. EMBOSS is produced by the European Molecular Biology Network (EMBnet - http://www.embnet.org/).

All EMBOSS tools are all built around the same set of core libraries - AJAX and NUCLEUS - and therefore share a unified user interface, have similar "look and feel", and implement a uniform sequence addressing methodology.

The various components of EMBOSS are distributed under the GPL, except the core libraries which are under the LGPL.

EMBASSY packages are third party applications which have been integrated with the EMBOSS suite, but which are not included in the base EMBOSS distribution for licensing or other reasons. The EMBASSY packages live in the biology/embassy port.

Install

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

pkg install biology/emboss
pkg install emboss

From the ports tree:

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

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

RUN_DEPENDS=	emboss>0:biology/emboss
LIB_DEPENDS=	libacd.so:biology/emboss

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	6.6.0_7	6.6.0_7	6.6.0_6	6.6.0_7	6.6.0_7
FreeBSD:14:quarterly	6.6.0_7	6.6.0_7	n/a	6.6.0_7	6.6.0_7
FreeBSD:15:latest	6.6.0_7	6.6.0_7	n/a	-	6.6.0_7
FreeBSD:15:quarterly	6.6.0_7	6.6.0_7	n/a	n/a	n/a
FreeBSD:16:latest	6.6.0_7	6.6.0_7	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

6.6.0_7

6.6.0_6

6.6.0_7

FreeBSD:14:quarterly

6.6.0_7

n/a

6.6.0_7

FreeBSD:15:latest

6.6.0_7

n/a

6.6.0_7

FreeBSD:15:quarterly

6.6.0_7

n/a

FreeBSD:16:latest

6.6.0_7

n/a

FreeBSD:16:quarterly

n/a

Dependencies

As this port's Makefile names them.

Build 2

clustalw : biology/clustalw
primer3 : biology/primer3

Library 2

libgd.so : graphics/gd
libpng.so : graphics/png

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

All build dependencies 38

All run dependencies 35

Required by 1

biology/biostar-tools

Configuration

Options name: biology_emboss

Option	Default	Description
DOCS	off	Build and/or install documentation
MYSQL	off	MySQL database support
X11	on	X11 (graphics) support

Option

Default

Description

DOCS

off

Build and/or install documentation

MYSQL

off

MySQL database support

X11

X11 (graphics) support

USES: gmake libtool iconv localbase:ldflags pgsql ssl
Service scripts: none
Conflicts with: qmail-ldap digest

Message after installing

The EMBOSS suite has been successfully installed under
 /usr/local/emboss

 To run EMBOSS programs make sure that /usr/local/emboss/bin is in your PATH.

 In order to see graphical output from some EMBOSS programs, you will
 need to set the following environment variable in your shell:

 set PLPLOT_LIB to: "/usr/local/emboss/share/EMBOSS"

 A sample configuration file has been installed in
 /usr/local/emboss/share/EMBOSS/emboss.default.template

 This must be renamed to emboss.default and edited to suit your site
 and requirements.

 A .embossrc file in a user's home directory overrides settings in the
 system-wide emboss.default.

 Additional third party applications for EMBOSS can be installed from the
 biology/embassy port. Remember, though that if you installed EMBOSS in a
 PREFIX other than the default, you will have to install EMBASSY into this
 same PREFIX.

Files

pkg-plist 2318

bin/aaindexextract
bin/abiview
bin/acdc
bin/acdgalaxy
bin/acdlog
bin/acdpretty
bin/acdtable
bin/acdtrace
bin/acdvalid
bin/aligncopy
bin/aligncopypair
bin/antigenic
bin/assemblyget
bin/backtranambig
bin/backtranseq
bin/banana
bin/biosed
bin/btwisted
bin/cachedas
bin/cachedbfetch
bin/cacheebeyesearch
bin/cacheensembl
bin/cai
bin/chaos
bin/charge
bin/checktrans
bin/chips
bin/cirdna
bin/codcmp
bin/codcopy
bin/coderet
bin/compseq
bin/cons
bin/consambig
bin/cpgplot
bin/cpgreport
bin/cusp
bin/cutgextract
bin/cutseq
bin/dan
bin/dbiblast
bin/dbifasta
bin/dbiflat
bin/dbigcg
bin/dbtell
bin/dbxcompress
bin/dbxedam
bin/dbxfasta
bin/dbxflat
bin/dbxgcg
bin/dbxobo
bin/dbxreport
bin/dbxresource
bin/dbxstat
bin/dbxtax
bin/dbxuncompress
bin/degapseq
bin/density
bin/descseq
bin/diffseq
bin/distmat
bin/dotmatcher
bin/dotpath
bin/dottup
bin/dreg
bin/drfinddata
bin/drfindformat
bin/drfindid
bin/drfindresource
bin/drget
bin/drtext
bin/edamdef
bin/edamhasinput
bin/edamhasoutput
bin/edamisformat
bin/edamisid
bin/edamname
bin/edialign
bin/einverted
%%LOCALBASE%%/bin/emboss
%%LOCALBASE%%/bin/emboss-shell
bin/embossdata
bin/embossupdate
bin/embossversion
bin/emma
bin/emowse
bin/entret
bin/epestfind
bin/eprimer3
bin/eprimer32
bin/equicktandem
bin/est2genome
bin/etandem
bin/extractalign
bin/extractfeat
bin/extractseq
bin/featcopy
bin/featmerge
bin/featreport
bin/feattext

The first 100 are listed.

distinfo 1

File	Size	SHA256
emboss/EMBOSS-6.6.0.tar.gz	1.17962028e+08	7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e

File

Size

SHA256

emboss/EMBOSS-6.6.0.tar.gz

1.17962028e+08

7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e

Master sites 1

ftp://emboss.open-bio.org/pub/EMBOSS/

Commit history 0

No commits in the history this site was built from.