sci-biology / samtools

Utilities for analysing and manipulating the SAM/BAM alignment formats

Official package sites : http://www.htslib.org/ ·

v1.9 :: 0 :: gentoo

Modified
License
MIT
Keywords
~amd64 ~amd64-linux ~x64-macos ~x86 ~x86-linux
USE flags
examples

v1.5 :: 0 :: gentoo

Modified
License
MIT
Keywords
~amd64 ~amd64-linux ~x64-macos ~x86 ~x86-linux
USE flags
examples

v0.1.20-r3 :: 0.1-legacy :: gentoo

Modified
License
MIT
Keywords
~amd64 ~amd64-linux ~x64-macos ~x86 ~x86-linux
USE flags
examples

General

examples
Install examples, usually source code

python_targets

python2_7
Build with Python 2.7

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

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

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

dev-lang / python-exec : Python script wrapper

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

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 / ncurses : console display library

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

virtual / pkgconfig : Virtual for the pkg-config implementation

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

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

dev-lang / python-exec : Python script wrapper

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

sys-libs / ncurses : console display library

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

dev-perl / Bio-SamTools : Read SAM/BAM database files

sci-biology / bedtools : Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats

sci-biology / consed : A genome sequence finishing program

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

Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: Version bump to 1.9
Bug: https://bugs.gentoo.org/647714 Signed-off-by: David Seifert <soap@gentoo.org> Package-Manager: Portage-2.3.50, Repoman-2.3.11
David Seifert · gentoo
sci-biology/samtools: Remove old
Bug: https://bugs.gentoo.org/show_bug.cgi?id=548170 Bug: https://bugs.gentoo.org/show_bug.cgi?id=620618 Bug: https://bugs.gentoo.org/show_bug.cgi?id=625504 Package-Manager: Portage-2.3.8, Repoman-2.3.3 Closes: https://github.com/gentoo/gentoo/pull/5593
David Seifert · gentoo
sci-biology/samtools: Version bump to 1.5
Package-Manager: Portage-2.3.8, Repoman-2.3.3
David Seifert · gentoo
sci-biology/samtools: [QA] Add missing python metadata variables
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/samtools: Use 'python-single-r1' instead of 'python-r1'
Package-Manager: portage-2.3.1
David Seifert · gentoo
sci-biology/samtools: Remove lua dep, fix perl shebangs
Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Remove lua dep, fix perl shebangs
Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: version bump to 1.3, to match htslib
* EAPI=6 * Added modern AX_WITH_CURSES that works with pkg-config * Fixed incorrect symlinks for libbam.so Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Move to SLOT="0.1-legacy" for future legacy versions
Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Add elog message discouraging direct use
Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Version bump to 0.1.20
* EAPI=6 * samtools will be slotted with SLOT="legacy", in order to be able to install applications that rely on the old monolithic library. Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Trim DESCRIPTION
* Add sub-slot operator for 'sys-libs/ncurses' dependency Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Trim DESCRIPTION
* Add sub-slot operator for 'sys-libs/ncurses' dependency Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Trim DESCRIPTION
* Add sub-slot operator for 'sys-libs/ncurses' dependency Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Trim DESCRIPTION
* Add sub-slot operator for 'sys-libs/ncurses' dependency Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Trim DESCRIPTION
* Add sub-slot operator for 'sys-libs/ncurses' dependency Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Trim DESCRIPTION
Package-Manager: portage-2.2.28
Agostino Sarubbo · gentoo
sci-biology/samtools: amd64 stable wrt bug #525630
Package-Manager: portage-2.2.20.1 RepoMan-Options: --include-arches="amd64"
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