sci-biology / tophat

Python-based splice junction mapper for RNA-Seq reads using bowtie2

Official package sites : https://ccb.jhu.edu/software/tophat/ ·

v2.1.1-r4 :: 0 :: gentoo

Modified
License
Artistic
Keywords
~amd64 ~x86
USE flags
debug

General

debug
Enable extra debug codepaths, like asserts and extra output. If you want to get meaningful backtraces see https://wiki.gentoo.org/wiki/Project:Quality_Assurance/Backtraces

python_targets

python2_7
Build with Python 2.7

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

dev-lang / python : An interpreted, interactive, object-oriented programming language

dev-lang / python-exec : Python script wrapper

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

dev-python / intervaltree : Editable interval tree data structure for Python 2 and 3

dev-python / sortedcontainers : Python library to sort collections and containers

sci-biology / bowtie : Popular short read aligner for Next-generation sequencing data

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

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

sys-devel / autoconf : Used to create autoconfiguration files

sys-devel / autoconf-archive : GNU Autoconf Macro Archive

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

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

virtual / pkgconfig : Virtual for the pkg-config implementation

dev-lang / python : An interpreted, interactive, object-oriented programming language

dev-lang / python-exec : Python script wrapper

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

dev-python / intervaltree : Editable interval tree data structure for Python 2 and 3

dev-python / sortedcontainers : Python library to sort collections and containers

sci-biology / bowtie : Popular short read aligner for Next-generation sequencing data

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

David Seifert · gentoo
sci-biology/tophat: Unbundle python modules
Bug: https://bugs.gentoo.org/show_bug.cgi?id=614370 Package-Manager: Portage-2.3.5, Repoman-2.3.2
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/tophat: Do not wrap scripts
Package-Manager: portage-2.3.1
David Seifert · gentoo
sci-biology/tophat: Remove old and ancient 1.0 ebuilds
Package-Manager: portage-2.3.1
David Seifert · gentoo
sci-biology/tophat: USE="threads" dep on dev-libs/boost
Gentoo-bug: 594810 * Remove autoconf macros from archive, depend on sys-devel/autoconf instead for the latest versions. Package-Manager: portage-2.3.1
David Seifert · gentoo
sci-biology/tophat: Allow for compiling with GCC 6
Gentoo-bug: 594544 Package-Manager: portage-2.3.1
David Seifert · gentoo
sci-biology/tophat: Various QA fixes, handle python properly
* Add subslot operator := for dev-libs/boost * DEPEND on virtual/pkgconfig * Add missing ${PYTHON_REQUIRED_USE} and ${PYTHON_DEPS} * Install python scripts and modules properly using 'python_doscript' and 'python_domodule' Package-Manager: portage-2.3.0
David Seifert · gentoo
sci-biology/tophat: Remove old and broken
Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/tophat: Version bump, use samtools:0.1-legacy
Gentoo-Bug: 545154, 546816, 566494, 572054 * EAPI=6 * Unbundle samtools and SeqAn * Fix broken shebangs in python scripts Package-Manager: portage-2.2.28
Sergey Popov · gentoo
sci-biology/tophat: correct dependency on sci-biology/seqan
Gentoo-Bug: 546816 Package-Manager: portage-2.2.20
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