notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)Want a good monitor light? See my photosAll times are UTC		 Ukraine
This referral link gives you 10% off a Fastmail.com account and gives me a discount on my Fastmail account.

Get notified when packages are built

A new feature has been added. FreshPorts already tracks package built by the FreeBSD project. This information is displayed on each port page. You can now get an email when FreshPorts notices a new package is available for something on one of your watch lists. However, you must opt into that. Click on Report Subscriptions on the right, and New Package Notification box, and click on Update.

Finally, under Watch Lists, click on ABI Package Subscriptions to select your ABI (e.g. FreeBSD:14:amd64) & package set (latest/quarterly) combination for a given watch list. This is what FreshPorts will look for.

Port details on branch 2022Q3
gatk Variant discovery in high-throughput sequencing data
4.5.0.0 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 4.5.0.0Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-12-03 08:41:01
Last Update: 2024-02-19 01:48:08
Commit Hash: 2ad82a1
Also Listed In: java
License: BSD3CLAUSE
WWW:
https://gatk.broadinstitute.org/hc/en-us
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (5 items)
Collapse this list.
  1. bin/gatk
  2. /usr/local/share/java/classes/GenomeAnalysisTK-4.5.0.0.jar
  3. /usr/local/share/licenses/gatk-4.5.0.0/catalog.mk
  4. /usr/local/share/licenses/gatk-4.5.0.0/LICENSE
  5. /usr/local/share/licenses/gatk-4.5.0.0/BSD3CLAUSE
Collapse this list.
Dependency lines:
  • gatk>0:biology/gatk
To install the port:
cd /usr/ports/biology/gatk/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/gatk
  • pkg install gatk
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: gatk
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1702890353 SHA256 (gatk-4.5.0.0-deps.tar.gz) = b6bf2e6ff9d64198e4ba185b2c09648bef841d274206603d0f6802e134b10cf5 SIZE (gatk-4.5.0.0-deps.tar.gz) = 883487836

Expand this list (2 items)

Collapse this list.

SHA256 (broadinstitute-gatk-4.5.0.0_GH0.tar.gz) = 39b09548ada317b29f19d6cbc0267301ee3565d575a5d79008a0168e679b98d2 SIZE (broadinstitute-gatk-4.5.0.0_GH0.tar.gz) = 104455420

Collapse this list.

Packages (timestamps in pop-ups are UTC):
gatk
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest4.5.0.04.5.0.0--4.5.0.0---
FreeBSD:13:quarterly4.5.0.04.5.0.0--4.5.0.0-4.5.0.04.5.0.0
FreeBSD:14:latest4.5.0.04.5.0.0--4.5.0.0--4.4.0.0
FreeBSD:14:quarterly4.5.0.04.5.0.0--4.5.0.0-4.5.0.04.5.0.0
FreeBSD:15:latest4.5.0.04.5.0.0n/a-n/a-4.5.0.0-
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gradle : devel/gradle
  2. java : java/openjdk17
  3. gettext-runtime>=0.22_1 : devel/gettext-runtime
Runtime dependencies:
  1. java : java/openjdk17
Library dependencies:
  1. libintl.so : devel/gettext-runtime
There are no ports dependent upon this port
Configuration Options:
===> The following configuration options are available for gatk-4.5.0.0: WITH_LARGE_FILES=off: Download large LFS files needed for build and tests ===> Use 'make config' to modify these settings
Options name:
biology_gatk
USES:
gettext-runtime
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/broadinstitute/gatk/tar.gz/4.5.0.0?dummy=/
Collapse this list.

There are no commits on branch 2022Q3 for this port
Login
User Login
Create account

Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD

This site
What is FreshPorts?
About the authors
Issues
FAQ
How big is it?
Security Policy
Privacy
Blog
Contact

Search
Enter Keywords:
 
more...

Latest Vulnerabilities
ruby31Apr 23
ruby32Apr 23
ruby33Apr 23
sdl2_soundApr 22
chromiumApr 21
ungoogled-chromiumApr 21
clamavApr 19
jenkinsApr 19
jenkins-ltsApr 19
electron27Apr 18
electron28Apr 18
electron29Apr 18
filezillaApr 16
php81Apr 16
php82Apr 16

16 vulnerabilities affecting 271 ports have been reported in the past 14 days

* - modified, not new

All vulnerabilities

Last processed:
2024-04-23 14:57:51 UTC


Ports
Home
Categories
Deleted ports
Sanity Test Failures
Newsfeeds

Statistics
Graphs
NEW Graphs (Javascript)

Calculated hourly:
Port count 32217
Broken 86
Deprecated 179
Ignore 217
Forbidden 2
Restricted 2
No CDROM 1
Vulnerable 40
Expired 5
Set to expire 153
Interactive 0
new 24 hours 1
new 48 hours3
new 7 days15
new fortnight24
new month125
Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD 		Valid HTML, CSS, and RSS. Copyright © 2000-2024 Dan Langille. All rights reserved.