Summary
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.
Versions
v6.6.0-r3 :: 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
USE flags
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
- 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
Dependencies
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
Runtime Dependencies
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
Depending packages
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-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
Bugs
- 549644
- sci-biology/emboss: try to install mimetype information
- 712504
- sci-biology/emboss-6.6.0-r2 : embossversion.c: error: _USE_FORTIFY_LEVEL undeclared (first use in this function)
- 920917
- sci-biology/emboss-6.6.0-r2 - ajreg.c: error: assignment to struct real_pcre from incompatible pointer type pcre {aka struct real_pcre8_or_16 } [-Winc
Change logs
- Repository mirror & CI · gentoo
Merge updates from master - David Seifert · gentoo
sci-biology/emboss: avoid file collision with dev-texlive/texlive-latexextra
Closes: https://bugs.gentoo.org/927976 Signed-off-by: David Seifert <soap@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Michał Górny · gentoo
Move {sys-devel → dev-build}/cons
Signed-off-by: Michał Górny <mgorny@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - David Seifert · gentoo
sci-biology/emboss: update EAPI 7 -> 8
Signed-off-by: David Seifert <soap@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - David Seifert · gentoo
sci-biology/emboss: Fix C99 `bool` clash
* Also fix `-Wimplicit-function-declaration` Closes: https://bugs.gentoo.org/695380 Signed-off-by: David Seifert <soap@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Andreas Sturmlechner · gentoo
sci-biology/emboss: EAPI-7 bump, minor style
Bug: https://bugs.gentoo.org/770262 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org> - 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