BSD Ports

biology/gatk 4.7.0.0 FreeBSD

Genome Analysis Toolkit

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
0767338087
License
BSD3CLAUSE
Categories
biology, java

Description

GATK, pronounced "Gee Ay Tee Kay" (not "Gat-Kay"), stands for GenomeAnalysisToolkit. It is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discovery. The tools can be used individually or chained together into complete workflows. end-to-end workflows are provided, called GATK Best Practices, tailored for specific use cases.

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

In the other systems

SystemPortVersion
FreeBSDbiology/gatk4.7.0.0
HardenedBSDbiology/gatk4.7.0.0
GhostBSDbiology/gatk4.7.0.0

Install

Binary package:

pkg install gatk

From the ports tree:

cd /usr/ports/biology/gatk/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	gatk>0:biology/gatk

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latest-4.7.0.0---
FreeBSD:14:quarterly-4.7.0.0n/a--
FreeBSD:15:latest-4.7.0.0n/a--
FreeBSD:15:quarterly-4.7.0.0n/an/an/a
FreeBSD:16:latest-4.7.0.0n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

As this port's Makefile names them.

Build 1

Runtime 3

The full lists below include those, and their dependencies in turn.

Build dependencies 63
Run dependencies 59

No port depends on this one.

Configuration

Options name: biology_gatk

OptionDefaultDescription
WITH_LARGE_FILESonDownload large LFS files needed for build and tests
USES
gettext-runtime java python:test
Service scripts
none

Files

distinfo 2
FileSizeSHA256
gatk-4.7.0.0-deps.tar.gz9.07471126e+0812875aab8f311d5e077f51b2ea12e2c38d3066b35ea4a0de26bf0fa294c1e74e
broadinstitute-gatk-4.7.0.0_GH0.tar.gz4.31894313e+099d42bfe74f7f5380eb2689a873ea00d27b16891b0cb7fd9deb10e1cfae553ec5

Commit history 2

DateCommitCreditsLog message
0767338087 Mathieu Arnold biology/gatk: fix fetch with new do-fetch.sh
6f260d6e70 Yuri Victorovich biology/gatk: update 4.6.2.0 → 4.7.0.0
ChangeLog: https://github.com/broadinstitute/gatk/releases/tag/4.7.0.0