sci-biology / augustus

Eukaryotic gene predictor

Official package sites : https://bioinf.uni-greifswald.de/augustus/ ·

v3.5.0 :: 0 :: gentoo

Modified
License
Artistic
Keywords
~amd64 ~x86
USE flags
doc test

v3.4.0-r3 :: 0 :: gentoo

Modified
License
Artistic
Keywords
amd64 ~x86
USE flags
doc

v2.5.5 :: 0 :: gentoo

Modified
License
Artistic
Keywords
amd64 ~x86
USE flags
examples

General

doc
Add extra documentation (API, Javadoc, etc). It is recommended to enable per package instead of globally
examples
Install examples, usually source code
test
Enable dependencies and/or preparations necessary to run tests (usually controlled by FEATURES=test but can be toggled independently)

dev-db / mysql++ : C++ API interface to the MySQL database

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

dev-db / sqlite : SQL database engine

dev-libs / boost : Boost Libraries for C++

sci-biology / bamtools : A programmer's API and an end-user's toolkit for handling BAM files

sci-biology / samtools : Utilities for analysing and manipulating the SAM/BAM alignment formats

sci-libs / gsl : The GNU Scientific Library

sci-libs / htslib : C library for high-throughput sequencing data formats

sci-libs / suitesparse : Metapackage for a suite of sparse matrix tools

sci-mathematics / lpsolve : Mixed Integer Linear Programming (MILP) solver

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

dev-db / mysql++ : C++ API interface to the MySQL database

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

dev-db / sqlite : SQL database engine

dev-libs / boost : Boost Libraries for C++

sci-biology / bamtools : A programmer's API and an end-user's toolkit for handling BAM files

sci-biology / samtools : Utilities for analysing and manipulating the SAM/BAM alignment formats

sci-libs / gsl : The GNU Scientific Library

sci-libs / htslib : C library for high-throughput sequencing data formats

sci-libs / suitesparse : Metapackage for a suite of sparse matrix tools

sci-mathematics / lpsolve : Mixed Integer Linear Programming (MILP) solver

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

868363
sci-biology/augustus-3.4.0-r3 calls g++ directly
873025
sci-biology/augustus-3.4.0-r2 fails tests (MUSL)
940693
sci-biology/augustus-2.5.5 - [ncurses-6.5] [libtool] [gcc-15] list.c: error: implicit declaration of function FatalError [-Wimplicit-function-declaration]
Repository mirror & CI · gentoo
Merge updates from master
Sam James · gentoo
sci-biology/augustus: Stabilize 3.4.0-r3 amd64, #920140
Signed-off-by: Sam James <sam@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
Alfred Wingate · gentoo
sci-biology/augustus: fix gcc15 build
Closes: https://bugs.gentoo.org/949617 Signed-off-by: Alfred Wingate <parona@protonmail.com> Closes: https://github.com/gentoo/gentoo/pull/40531 Signed-off-by: Sam James <sam@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
Sam James · gentoo
sci-biology/augustus: fix phase definition order
... to match execution order. Signed-off-by: Sam James <sam@gentoo.org>
Alfred Wingate · gentoo
sci-biology/augustus: include cstdint for gcc-13
Closes: https://bugs.gentoo.org/895204 Signed-off-by: Alfred Wingate <parona@protonmail.com> Signed-off-by: Sam James <sam@gentoo.org>
Alfred Wingate · gentoo
sci-biology/augustus: add 3.5.0
* Add missing dependency on python with tests. * Wire up unittests. * Disable test comparing on musl. This follows upstream with non-amd64 and non-linux environments. Bug: https://bugs.gentoo.org/868363 Bug: https://bugs.gentoo.org/873025 Signed-off-by: Alfred Wingate <parona@protonmail.com> Closes: https://github.com/gentoo/gentoo/pull/40521 Signed-off-by: Sam James <sam@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
Arthur Zamarin · gentoo
sci-biology/augustus: destabilize for ~x86
Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
Sam James · gentoo
sci-biology/augustus: add lpsolve subslot dep
Bug: https://bugs.gentoo.org/614866 Signed-off-by: Sam James <sam@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
Sam James · gentoo
sci-biology/augustus: respect CC, CXX
Closes: https://bugs.gentoo.org/832187 Signed-off-by: Sam James <sam@gentoo.org>
Sam James · gentoo
sci-biology/augustus: fix Boost dep
Closes: https://bugs.gentoo.org/864773 Signed-off-by: Sam James <sam@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
Andrew Ammerlaan · gentoo
sci-biology/augustus: add forgotten runtime dependency
Closes: https://bugs.gentoo.org/832186 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
Andrew Ammerlaan · gentoo
sci-biology/augustus: add version 3.4.0
Closes: https://bugs.gentoo.org/515996 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/augustus: Port to EAPI 7
Package-Manager: Portage-2.3.81, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
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