| Port details |
- gatk Genome Analysis Toolkit
- 4.6.1.0_1 biology
 =2      4.6.1.0_1Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2018-12-03 08:41:01
- Last Update: 2025-02-14 10:30:52
- Commit Hash: feb6d32
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: java
- License: BSD3CLAUSE
- WWW:
- https://gatk.broadinstitute.org/hc/en-us
- https://github.com/broadinstitute/gatk
- 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.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- 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 = 1730356703
SHA256 (gatk-4.6.1.0-deps.tar.gz) = ea0205776f26bbe51bcdea6dd10df975a2e4861a772901523ff7ab123119b8ad
SIZE (gatk-4.6.1.0-deps.tar.gz) = 922113997
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- gradle8 : devel/gradle8
- gettext-runtime>=0.22_1 : devel/gettext-runtime
- java : java/openjdk17
- Test dependencies:
-
- python3.11 : lang/python311
- Runtime dependencies:
-
- libfml.so : biology/fermi-lite
- gkl>0 : biology/gkl
- mummer>0 : biology/mummer
- java : java/openjdk17
- Library dependencies:
-
- libintl.so : devel/gettext-runtime
- Fetch dependencies:
-
- git : devel/git
- git-lfs : devel/git-lfs
- There are no ports dependent upon this port
Configuration Options:- ===> The following configuration options are available for gatk-4.6.1.0_1:
WITH_LARGE_FILES=on: Download large LFS files needed for build and tests
===> Use 'make config' to modify these settings
- Options name:
- biology_gatk
- USES:
- gettext-runtime java python:test
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
4.6.1.0_1
14 Feb 2025 10:30:52
 |
Yuri Victorovich (yuri) |
biology/gatk: Update WWW |
4.6.1.0_1
06 Feb 2025 15:05:37
|
Yuri Victorovich (yuri) |
biology/gatk: Fix build breakage after gradle update to 8.12.1
Reported by: fallout |
4.6.1.0_1
31 Dec 2024 08:57:55
|
Muhammad Moinur Rahman (bofh) |
Mk/**java.mk: Convert bsd.java.mk to USES
The following features have been added or changed:
- Instead of USE_JAVA use USES=java. This defaults to
USES=java:build,run if NO_BUILD is undefined. Else it defaults to
USES=java:run
- Instead of USE_ANT=yes use USES=java:ant which also implies
USES=java:build
- Instead of JAVA_BUILD=yes use USES=java:build. Does not imply run or
extract
- Instead of JAVA_EXTRACT=yes use USES=java:extract does not imply
build or run
- Instead of JAVA_RUN=yes use USES=java:run does not imply extract or
build
- Instead of USE_JAVA=<version> use USES=java and JAVA_VERSION=<version>
Approved by: mat (portmgr), glewis
Differential Revision: https://reviews.freebsd.org/D48201 |
4.6.1.0_1
01 Nov 2024 19:29:28
|
Yuri Victorovich (yuri) |
biology/gatk: Update TEST_ENV |
4.6.1.0_1
31 Oct 2024 19:28:13
|
Yuri Victorovich (yuri) |
biology/gatk: Update tests stats; Add dependency |
4.6.1.0
31 Oct 2024 08:28:18
|
Yuri Victorovich (yuri) |
biology/gatk: update 4.6.0.0 → 4.6.1.0 |
4.6.0.0_1
04 Aug 2024 20:13:15
|
Yuri Victorovich (yuri) |
biology/gatk: Update COMMENT |
4.6.0.0_1
04 Aug 2024 20:07:19
|
Yuri Victorovich (yuri) |
biology/gatk: Add dependencies biology/fermi-lite and biology/gkl; Add python
dependency for tests |
4.6.0.0
20 Jul 2024 08:36:53
|
Yuri Victorovich (yuri) |
biology/gatk: Fix fetch |
4.6.0.0
14 Jul 2024 16:32:42
|
Yuri Victorovich (yuri) |
biology/gatk: Fix fetch
Reported by: fallout |
4.6.0.0
13 Jul 2024 18:35:06
|
Yuri Victorovich (yuri) |
biology/gatk: Prevent execution of git hooks from $DISTDIR during fetch |
4.6.0.0
12 Jul 2024 03:51:21
|
Yuri Victorovich (yuri) |
biology/gatk: update 4.5.0.0 → 4.6.0.0 |
4.5.0.0
19 Feb 2024 01:48:08
|
Yuri Victorovich (yuri) |
*/*: Replace format=bsdtar with format=ustar in tar archive operations
... because the undocumented format bsdtar adds paxheaders on
some systems, therefore breaking the fetch.
The documentation for format=bsdtar should be added:
https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=277139
Approved by: portmgr (blanket unbreak) |
4.5.0.0
31 Dec 2023 00:37:05
|
Muhammad Moinur Rahman (bofh) |
*/*: Sunset 12.4-RELEASE/12-STABLE from ports tree
- Remove all references to defunct ARCH arm
- Remove all references to defunct ARCH sparc64
- Remove x11-drivers/xf86-video-sunffb which requires defunct sparc64
ARCH
- Remove sysutils/afbinit requires defunct sparc64 ARCH
- Remove all references to bktr driver
- Remove all references to defunct FreeBSD_12
- Remove all references to OSVERSION/OSREL corresponding to 12
- Remove conditionals in Mk/Uses/cabal.mk
- Remove sparc reference from Mk/Uses/qt-dist.mk
- Remove BROKEN_sparc64/NOT_FOR_ARCH=sparc64
- Remove BROKEN_FreeBSD_12* from:
- Remove OpenSSL patches from:
- Remove conditional flags for OSVERSION >= 1300000 to fixed flags.
Also move conditional flags for non sparc64/arm ARCH to fixed flags.
Reviewed by: brooks, jbeich, rene, salvadore
Differential Revision: https://reviews.freebsd.org/D42068 |
4.5.0.0
18 Dec 2023 09:14:18
|
Yuri Victorovich (yuri) |
biology/gatk: update 4.4.0.0 → 4.5.0.0
ChangeLog: https://github.com/broadinstitute/gatk/releases/tag/4.5.0.0 |
4.4.0.0
04 Jun 2023 22:02:58
|
Yuri Victorovich (yuri) |
biology/gatk: Update 4.3.0.0 → 4.4.0.0 |
4.3.0.0
27 Nov 2022 04:06:47
|
Yuri Victorovich (yuri) |
biology/gatk: Update 4.2.6.1 -> 4.3.0.0 |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
4.2.6.1_1
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above  ) |
4.2.6.1_1
11 Aug 2022 18:33:41
|
Dmitry Marakasov (amdmi3) |
biology/gatk: mark BROKEN
FAILURE: Build failed with an exception.
* Where:
Build file '/wrkdirs/usr/ports/biology/gatk/work/gatk-4.2.6.1/build.gradle'
line: 15
* What went wrong:
Plugin [id: 'de.undercouch.download', version: '4.1.2'] was not found in any of
the following sources:
- Gradle Core Plugins (plugin is not in 'org.gradle' namespace)
- Plugin Repositories (could not resolve plugin artifact
'de.undercouch.download:de.undercouch.download.gradle.plugin:4.1.2')
Searched in the following repositories:
Gradle Central Plugin Repository
Reported by: pkg-fallout
Approved by: portmgr blanket |
4.2.6.1_1
24 May 2022 22:39:38
|
Yuri Victorovich (yuri) |
biology/gatk: Use Java 17 instead of EOLed Java 12 |
4.2.6.1
23 May 2022 02:05:40
|
Yuri Victorovich (yuri) |
biology/gatk: Update 4.2.6.0 -> 4.2.6.1 |
4.2.6.0
10 Apr 2022 23:21:50
|
Yuri Victorovich (yuri) |
biology/gatk: Update 4.2.0.0 -> 4.2.6.0 |
4.2.0.0
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
4.2.0.0
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
4.2.0.0
13 Mar 2021 18:55:15
 |
yuri |
biology/gatk: Fix fetch
Reported by: fallout |
4.2.0.0
12 Mar 2021 04:27:49
|
yuri |
biology/gatk: Update 4.1.9.0 -> 4.2.0.0 |
4.1.9.0_1
22 Jan 2021 02:50:38
|
yuri |
biology/gatk: Add the WITH_LARGE_FILES option. |
4.1.9.0
21 Jan 2021 23:15:40
|
yuri |
biology/gatk: Update 4.1.8.1 -> 4.1.9.0 |
4.1.8.1
08 Sep 2020 19:25:37
|
yuri |
biology/gatk: Fix build
For some reason the -deps archive had a wrong size, perhaps because it was
regenerated and not uploaded.
-deps was generated by me.
Updating distinfo.
Reported by: fallout |
4.1.8.1
06 Sep 2020 02:16:45
|
yuri |
biology/gatk: Update 4.1.8.0 -> 4.1.8.1 |
4.1.8.0
09 Jul 2020 00:40:56
|
yuri |
biology/gatk: Update 4.1.7.0 -> 4.1.8.0 |
4.1.7.0
28 May 2020 02:26:52
|
yuri |
biology/gatk: Update 4.1.5.0 -> 4.1.7.0 |
4.1.5.0
26 May 2020 03:37:48
|
linimon |
Mark as BROKEN on powerpc64 12. It builds on -head.
While here, pet portlint (remove extra blank line).
Approved by: portmgr (tier-2 blanket) |
4.1.5.0
06 May 2020 13:11:49
|
tobik |
Preserve Gradle 6.2.2 for biology/gatk
It fails to build with newer Gradle versions again. |
4.1.5.0
04 Mar 2020 08:47:55
|
yuri |
biology/gatk: Update 4.1.4.1 -> 4.1.5.0
Reported by: repology |
4.1.4.1_1
09 Feb 2020 05:57:04
|
yuri |
biology/gatk: Change from gradle5 to gradle6 |
4.1.4.1
20 Jan 2020 02:12:37
|
yuri |
biology/gatk: Update 4.1.3.0 -> 4.1.4.1 |
4.1.3.0
05 Jan 2020 10:33:09
|
yuri |
biology/gatk: Update 4.1.2.0-43 -> 4.1.3.0
Reported by: repology |
4.1.2.0.43
20 Nov 2019 09:51:43
|
tobik |
Create devel/gradle5 in preparation of devel/gradle update
Many consumers fail to build with newer Gradle versions.
PR: 239875, 239900, 239901, 239902 |
4.1.2.0.43
26 Jul 2019 18:03:09
|
yuri |
biology/gatk: Update 4.0.11.0 -> 4.1.2.0-43
Now it builds with gradle-5.
Improvements im Makefile to simplify the port update process, in line with some
other gradle-based ports.
Reported by: repology |
4.0.11.0
23 Jul 2019 05:28:46
|
tobik |
Prepare for devel/gradle4 and java/openjfx8-devel updates
openjfx8-devel now requires at least Gradle 4.8. biology/gatk
however does not build with Gradle 4.10.3. Preserve Gradle 4.6 for
now.
PR: 239392 |
4.0.11.0
04 Dec 2018 17:53:46
|
yuri |
devel/gradle: Update to 5.0
Change biology/igv and biology/gatk to gradle4 due to build failures with
gradle5.
PR: 233623
Approved by: gasol.wu@gmail.com (maintainer) |
4.0.11.0
03 Dec 2018 23:04:24
|
yuri |
biology/gatk: Change gradle4->gradle because it builds fine with both gradle 4
and 5 |
4.0.11.0
03 Dec 2018 08:52:03
|
yuri |
biology/gatk: Correct the target |
4.0.11.0
03 Dec 2018 08:40:53
|
yuri |
New port: biology/gatk: Variant discovery in high-throughput sequencing data |
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