sci-biology / emboss

The European Molecular Biology Open Software Suite - A sequence analysis package

Official package sites : http://emboss.sourceforge.net/ ·

EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.

v6.6.0-r1 :: 0 :: gentoo

Modified
License
LGPL-2 GPL-2 Apache-2.0 GPL-3+ CC-BY-3.0
Keywords
~amd64 ~amd64-linux ~x86 ~x86-linux
USE flags
X minimal mysql pdf png postgres static-libs

General

X
Add support for X11
minimal
Install a very minimal build (disables, for example, plugins, fonts, most drivers, non-critical features)
mysql
Add mySQL Database support
pdf
Add general support for PDF (Portable Document Format), this replaces the pdflib and cpdflib flags
png
Add support for libpng (PNG images)
postgres
Add support for the postgresql database
static-libs
Build static versions of dynamic libraries as well

app-portage / elt-patches : Collection of patches for libtool.eclass

dev-db / mysql-connector-c : C client library for MariaDB/MySQL

dev-db / postgresql : PostgreSQL RDBMS

dev-libs / expat : Stream-oriented XML parser library

dev-libs / libpcre : Perl-compatible regular expression library

media-libs / gd : Graphics library for fast image creation

media-libs / libharu : C/C++ library for PDF generation

sci-libs / plplot : Multi-language scientific plotting library

sys-devel / autoconf : Used to create autoconfiguration files

sys-devel / automake : Used to generate Makefile.in from Makefile.am

sys-devel / libtool : A shared library tool for developers

sys-libs / zlib : Standard (de)compression library

x11-libs / libXt : X.Org X Toolkit Intrinsics library

dev-db / mysql-connector-c : C client library for MariaDB/MySQL

dev-db / postgresql : PostgreSQL RDBMS

dev-libs / expat : Stream-oriented XML parser library

dev-libs / libpcre : Perl-compatible regular expression library

games-action / xbomber : Bomberman clone w/multiplayer support

media-libs / gd : Graphics library for fast image creation

media-libs / libharu : C/C++ library for PDF generation

sci-libs / plplot : Multi-language scientific plotting library

sys-devel / cons : Extensible perl-based build utility

sys-libs / zlib : Standard (de)compression library

x11-libs / libXt : X.Org X Toolkit Intrinsics library

dev-java / emma : Free Java code coverage tool

games-action / xbomber : Bomberman clone w/multiplayer support

sci-biology / aaindex : Amino acid indices and similarity matrices

sci-biology / cutg : Codon usage tables calculated from GenBank

sci-biology / embassy-cbstools : EMBOSS integrated version of Applications from the CBS group

sci-biology / embassy-clustalomega : EMBOSS integrated version of Clustal Omega - Multiple Sequence Alignment

sci-biology / embassy-domainatrix : EMBOSS integrated version of Protein domain analysis add-on package

sci-biology / embassy-domalign : EMBOSS integrated version of Protein domain alignment add-on package

sci-biology / embassy-domsearch : EMBOSS integrated version of Protein domain search add-on package

sci-biology / embassy-emnu : EMBOSS integrated version of Simple menu of EMBOSS applications

sci-biology / embassy-esim4 : EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA

sci-biology / embassy-hmmer : EMBOSS integrated version of HMMER wrapper - sequence analysis with profile HMMs

sci-biology / embassy-iprscan : EMBOSS integrated version of InterProScan motif detection add-on package

sci-biology / embassy-meme : EMBOSS integrated version of MEME - Multiple Em for Motif Elicitation

sci-biology / embassy-mse : EMBOSS integrated version of MSE - Multiple Sequence Screen Editor

sci-biology / embassy-phylipnew : EMBOSS integrated version of The Phylogeny Inference Package

sci-biology / embassy-signature : EMBOSS integrated version of Protein signature add-on package

sci-biology / embassy-structure : EMBOSS integrated version of Protein structure add-on package

sci-biology / embassy-topo : EMBOSS integrated version of Transmembrane protein display

sci-biology / embassy-vienna : EMBOSS integrated version of Vienna RNA package - RNA folding

sci-biology / prints : A protein motif fingerprint database

sci-biology / prosite : A protein families and domains database

sci-biology / rebase : A restriction enzyme database

sci-biology / shrimp : SHort Read Mapping Package

sci-biology / transfac : A database of eucaryotic transcription factors

sys-devel / cons : Extensible perl-based build utility

549644
sci-biology/emboss: try to install mimetype information
610066
sci-biology/emboss-6.6.0-r1 : libtool: error: cannot determine absolute directory name of 'lib64'
Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
David Seifert · gentoo
sci-biology/emboss: Remove old
Package-Manager: Portage-2.3.3, Repoman-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/3937
David Seifert · gentoo
sci-biology/emboss: Port to emboss-r2.eclass
Package-Manager: portage-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/3937
David Seifert · gentoo
sci-biology/emboss: Remove ppc from KEYWORDS
Package-Manager: Portage-2.3.3, Repoman-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/3856
Austin English · gentoo
sci-biology/emboss: add a blocker for games-action/xbomber #589918
Gentoo-Bug: https://bugs.gentoo.org/589918 Package-Manager: portage-2.3.0
Justin Lecher · gentoo
sci-biology/emboss: Clean up of files dir
Move to readme.gentoo-r1.eclass Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=579728 Package-Manager: portage-2.2.28 Signed-off-by: Justin Lecher <jlec@gentoo.org>
Justin Lecher · gentoo
sci-biology/emboss: Drop old
obsolets multiple bugs Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=542274 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=534418 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=521604 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=514014 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=493724 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=406279 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=393311 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=382321 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=378443 Package-Manager: portage-2.2.20.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
Manuel Rüger · gentoo
sci-biology/emboss: Restore old version.
This commit reverts 0d040c84fbb38ead35451769d2b65a33af2fbf2a. Package-Manager: portage-2.2.20.1 RepoMan-Options: --force
Mikle Kolyada · gentoo
sci-biology/emboss: Drop old
Package-Manager: portage-2.2.20.1
Mikle Kolyada · gentoo
sci-biology/emboss: x86 stable wrt bug #529038
Package-Manager: portage-2.2.20.1
Mikle Kolyada · gentoo
sci-biology/emboss: amd64 stable wrt bug #529038
Package-Manager: portage-2.2.20.1
Robin H. Johnson · gentoo
proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed