sci-biology / picard

Java-based command-line utilities that manipulate SAM files

Official package sites : http://picard.sourceforge.net/ ·

v1.103 :: 0 :: gentoo

Modified
License
Apache-2.0
Keywords
~amd64 ~x86
USE flags
doc source test

General

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

elibc

FreeBSD
ELIBC setting for systems that use the FreeBSD C library

app-arch / zip : Info ZIP (encryption support)

dev-java / ant-apache-bcel : Apache Ant's optional tasks depending on bcel

dev-java / ant-core : Java-based build tool similar to 'make' that uses XML configuration files

dev-java / ant-junit4 : Apache Ant's optional tasks depending on junit-4

dev-java / cofoja : Contracts for Java

dev-java / commons-jexl : Expression language engine, can be embedded in applications and frameworks

dev-java / java-config : Java environment configuration query tool

dev-java / javatoolkit : Collection of Gentoo-specific tools for Java

dev-java / snappy : Snappy compressor/decompressor for Java

dev-java / testng : Testing framework inspired by JUnit and NUnit with new features

dev-lang / R : Language and environment for statistical computing and graphics

virtual / jdk : Virtual for Java Development Kit (JDK)

app-arch / zip : Info ZIP (encryption support)

dev-java / ant-core : Java-based build tool similar to 'make' that uses XML configuration files

dev-java / cofoja : Contracts for Java

dev-java / commons-jexl : Expression language engine, can be embedded in applications and frameworks

dev-java / java-config : Java environment configuration query tool

dev-java / snappy : Snappy compressor/decompressor for Java

virtual / jre : Virtual for Java Runtime Environment (JRE)

572142
sci-biology/picard - Tests fail and download a LOT of data from www.broadinstitute.org
580176
sci-biology/picard-2.19.2 version bump
671632
sci-biology/picard - error: no main manifest attribute, in /usr/share/picard/lib/picard.jar
Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
Justin Lecher · gentoo
Use https by default
Convert all URLs for sites supporting encrypted connections from http to https Signed-off-by: Justin Lecher <jlec@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