sci-biology / bowtie

Popular short read aligner for Next-generation sequencing data

Official package sites : http://bowtie-bio.sourceforge.net/bowtie2/ ·

v2.2.9 :: 2 :: gentoo

Modified
License
GPL-3
Keywords
~amd64 ~x86
USE flags
examples tbb

v1.1.2-r1 :: 1 :: gentoo

Modified
License
Artistic
Keywords
~amd64 ~x64-macos ~x86
USE flags
examples tbb

General

examples
Install examples, usually source code
tbb
Enables building bowtie with the Intel Threading Building Blocks from dev-cpp/tbb. This flag is recommended.

cpu_flags_x86

sse2
Use the SSE2 instruction set

app-arch / unzip : unzipper for pkzip-compressed files

dev-cpp / tbb : High level abstract threading library

dev-lang / perl : Larry Wall's Practical Extraction and Report Language

sci-biology / seqan : C++ Sequence Analysis Library

dev-cpp / tbb : High level abstract threading library

dev-lang / perl : Larry Wall's Practical Extraction and Report Language

sci-biology / tophat : Python-based splice junction mapper for RNA-Seq reads using bowtie2

David Seifert · gentoo
sci-biology/bowtie: Remove old
Closes: https://bugs.gentoo.org/630140 Package-Manager: Portage-2.3.19, Repoman-2.3.6 Closes: https://github.com/gentoo/gentoo/pull/6626
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/bowtie: Allow for compiling with GCC 6
Gentoo-bug: 593966 Package-Manager: portage-2.3.0
David Seifert · gentoo
sci-biology/bowtie: version bump
Package-Manager: portage-2.3.0_rc1
David Seifert · gentoo
sci-biology/bowtie: Version bump to 2.2.8
* EAPI=6 Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/bowtie: unbundle SeqAn, import Debian patches
* EAPI=6 Package-Manager: portage-2.2.28
Justin Lecher · gentoo
sci-biology/bowtie: Chop DESCRIPTION to 80 chars
Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
Justin Lecher · gentoo
sci-biology/bowtie: Drop old
obsoletes: Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=564320 Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
Agostino Sarubbo · gentoo
sci-biology/bowtie: x86 stable wrt bug #569706
Package-Manager: portage-2.2.24 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
Agostino Sarubbo · gentoo
sci-biology/bowtie: x86 stable wrt bug #569708
Package-Manager: portage-2.2.24 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
Agostino Sarubbo · gentoo
sci-biology/bowtie: amd64 stable wrt bug #569706
Package-Manager: portage-2.2.24 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
Agostino Sarubbo · gentoo
sci-biology/bowtie: amd64 stable wrt bug #569708
Package-Manager: portage-2.2.24 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
Justin Lecher · gentoo
sci-biology/bowtie: Respect CXX
Package-Manager: portage-2.2.23 Signed-off-by: Justin Lecher <jlec@gentoo.org>
Ted Tanberry · gentoo
sci-biology/bowtie: bring back stable bowtie-0.12.8
bowtie-0.12.8 is the only stable variant and removing it breaks the stable depgraph.
Ted Tanberry · gentoo
sci-biology/bowtie-2.2.6: Enable 'tbb' USE flag by default
Ted Tanberry · gentoo
sci-biology/bowtie-1.1.2: Enable 'tbb' USE flag by default
Ted Tanberry · gentoo
sci-biology/bowtie: remove REQUIRED_USE
When SSE2 support is not explicitly enabled, the user is informed by erroring out instead of portage recommending enabling cpu flags.
Ted Tanberry · gentoo
sci-biology/bowtie: do not remove -Wall from CXXFLAGS
Retain -Wall in CXXFLAGS in bowtie-1.1.2
Ted Tanberry · gentoo
sci-biology/bowtie: Add bowtie2 in SLOT=2
Ted Tanberry · gentoo
sci-biology/bowtie: version bump, SLOT major version
sci-biology/bowtie is now SLOTed, in order to allow for a parallel installation with bowtie2. In addition, the latest bowtie now supports dev-cpp/tbb with 'tbb' USE flag.
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