sci-biology / bioperl

Perl tools for bioinformatics - Core modules

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

v9999-r1 :: 0 :: gentoo

Modified
License
Artistic GPL-2
USE flags
db graphviz minimal network run

v1.6.9 :: 0 :: gentoo

Modified
License
|| ( Artistic GPL-1+ )
Keywords
amd64 x86
USE flags
db graphviz minimal network run sqlite

General

db
Install sci-biology/bioperl-run
graphviz
Add support for the Graphviz library
minimal
Install a very minimal build (disables, for example, plugins, fonts, most drivers, non-critical features)
network
Install sci-biology/bioperl-run
run
Install sci-biology/bioperl-run
sqlite
Add support for sqlite - embedded sql database

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

dev-perl / Ace : Object-Oriented Access to ACEDB Databases

dev-perl / Algorithm-Munkres : Munkres solution to classical Assignment problem

dev-perl / Array-Compare : Perl extension for comparing arrays

dev-perl / Bio-ASN1-EntrezGene : Regular expression-based Perl Parser for NCBI Entrez Gene

dev-perl / Clone : Recursively copy Perl datatypes

dev-perl / Convert-Binary-C : Binary Data Conversion using C Types

dev-perl / DBD-SQLite : Self Contained RDBMS in a DBI Driver

dev-perl / Data-Stag : Structured Tags datastructures

dev-perl / GD : Interface to Thomas Boutell's gd library

dev-perl / Graph : Data structure and ops for directed graphs

dev-perl / GraphViz : Interface to AT&T's GraphViz

dev-perl / HTML-Parser : Parse <HEAD> section of HTML documents

dev-perl / List-MoreUtils : Provide the missing functionality from List::Util

dev-perl / Math-Random : Random Number Generators

dev-perl / Module-Build : Build and install Perl modules

dev-perl / PostScript : An object that may be used to construct a block of text in PostScript

dev-perl / SOAP-Lite : Lightweight interface to the SOAP protocol both on client and server side

dev-perl / SVG : Perl extension for generating Scalable Vector Graphics (SVG) documents

dev-perl / SVG-Graph : Visualize your data in Scalable Vector Graphics (SVG) format

dev-perl / Set-Scalar : Scalar set operations

dev-perl / Sort-Naturally : sort lexically, but sort numeral parts numerically

dev-perl / Spreadsheet-ParseExcel : Read information from an Excel file

dev-perl / Spreadsheet-WriteExcel : Write cross-platform Excel binary file

dev-perl / URI : Uniform Resource Identifiers (absolute and relative)

dev-perl / XML-DOM : A Perl module for an DOM Level 1 compliant interface

dev-perl / XML-DOM-XPath : Perl extension to add XPath support to XML::DOM, using XML::XPath engine

dev-perl / XML-Parser : A Perl extension interface to James Clark's XML parser, expat

dev-perl / XML-SAX : Perl module for using and building Perl SAX2 XML parsers, filters, and drivers

dev-perl / XML-Simple : An API for simple XML files

dev-perl / XML-Twig : Process huge XML documents in tree mode

dev-perl / XML-Writer : XML Writer Perl Module

dev-perl / XML-XPath : A XPath Perl Module

dev-perl / YAML : YAML Ain't Markup Language (tm)

dev-perl / libwww-perl : A collection of Perl Modules for the WWW

dev-vcs / git : stupid content tracker: distributed VCS designed for speed and efficiency

virtual / perl-Storable : Virtual for Storable

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

dev-perl / Ace : Object-Oriented Access to ACEDB Databases

dev-perl / Algorithm-Munkres : Munkres solution to classical Assignment problem

dev-perl / Array-Compare : Perl extension for comparing arrays

dev-perl / Bio-ASN1-EntrezGene : Regular expression-based Perl Parser for NCBI Entrez Gene

dev-perl / Clone : Recursively copy Perl datatypes

dev-perl / Convert-Binary-C : Binary Data Conversion using C Types

dev-perl / DBD-SQLite : Self Contained RDBMS in a DBI Driver

dev-perl / Data-Stag : Structured Tags datastructures

dev-perl / GD : Interface to Thomas Boutell's gd library

dev-perl / Graph : Data structure and ops for directed graphs

dev-perl / GraphViz : Interface to AT&T's GraphViz

dev-perl / HTML-Parser : Parse <HEAD> section of HTML documents

dev-perl / List-MoreUtils : Provide the missing functionality from List::Util

dev-perl / Math-Random : Random Number Generators

dev-perl / PostScript : An object that may be used to construct a block of text in PostScript

dev-perl / SOAP-Lite : Lightweight interface to the SOAP protocol both on client and server side

dev-perl / SVG : Perl extension for generating Scalable Vector Graphics (SVG) documents

dev-perl / SVG-Graph : Visualize your data in Scalable Vector Graphics (SVG) format

dev-perl / Set-Scalar : Scalar set operations

dev-perl / Sort-Naturally : sort lexically, but sort numeral parts numerically

dev-perl / Spreadsheet-ParseExcel : Read information from an Excel file

dev-perl / Spreadsheet-WriteExcel : Write cross-platform Excel binary file

dev-perl / URI : Uniform Resource Identifiers (absolute and relative)

dev-perl / XML-DOM : A Perl module for an DOM Level 1 compliant interface

dev-perl / XML-DOM-XPath : Perl extension to add XPath support to XML::DOM, using XML::XPath engine

dev-perl / XML-Parser : A Perl extension interface to James Clark's XML parser, expat

dev-perl / XML-SAX : Perl module for using and building Perl SAX2 XML parsers, filters, and drivers

dev-perl / XML-Simple : An API for simple XML files

dev-perl / XML-Twig : Process huge XML documents in tree mode

dev-perl / XML-Writer : XML Writer Perl Module

dev-perl / XML-XPath : A XPath Perl Module

dev-perl / YAML : YAML Ain't Markup Language (tm)

dev-perl / libwww-perl : A collection of Perl Modules for the WWW

virtual / perl-Storable : Virtual for Storable

dev-perl / Bio-ASN1-EntrezGene : Regular expression-based Perl Parser for NCBI Entrez Gene

dev-perl / Bio-DB-HTS : Perl bindings for sci-libs/htslib

dev-perl / Bio-Das : Interface to Distributed Annotation System

dev-perl / Bio-Graphics : Generate images from Bio::Seq objects for visualization purposes

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

sci-biology / GBrowse : Generic Model Organism Database Project - The Generic Genome Browser

sci-biology / bioperl-db : Perl tools for bioinformatics - Perl API that accesses the BioSQL schema

sci-biology / bioperl-network : Perl tools for bioinformatics - Analysis of protein-protein interaction networks

sci-biology / bioperl-run : Perl wrapper modules for key bioinformatics applications

sci-biology / diya : Do It Yourself Annotation, tools & libraries for sequence assembly & annotation

145580
sci-biology/bioperl: tests require several perl modules not in portage yet
514916
sci-biology/bioperl should install executable tools from examples
547018
sci-biology/bioperl-1.6.9 dev-perl/Bio-ASN1-EntrezGene-1.91.0-r1 circular dependencies
566466
sci-biology/bioperl: introduce USE=staden flag so that newer versions of io_lib can be installed
600826
sci-biology/bioperl: Package uses dev-perl/XML-Twig and makes no clear statement regarding handling of external entities (CVE-2016-9180)
David Hicks · gentoo
sci-biology/bioperl: use HTTPS for GitHub
Package-Manager: Portage-2.3.6, Repoman-2.3.3
Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
Kent Fredric · gentoo
sci-biology/bioperl: Fix dependency on dev-perl/YAML
Package-Manager: portage-2.2.28 RepoMan-Options: --include-arches="alpha amd64 amd64-fbsd arm arm64 hppa ia64 m68k mips nios2 ppc ppc64 riscv s390 sh sparc sparc-fbsd x86 x86-fbsd"
Kent Fredric · gentoo
sci-biology/bioperl: Fix dependency on dev-perl/Set-Scalar
Package-Manager: portage-2.2.28 RepoMan-Options: --include-arches="amd64 amd64-fbsd arm arm64 mips nios2 ppc ppc64 riscv s390 sh sparc-fbsd"
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