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Port details
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.


No package information for this port in our database
Sometimes this happens. Not all ports have packages.
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.

Number of commits found: 34

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
4.5.0.0
19 Feb 2024 01:48:08
commit hash: 2ad82a1068e1e06f47843bbbb7df1e281bd53d29commit hash: 2ad82a1068e1e06f47843bbbb7df1e281bd53d29commit hash: 2ad82a1068e1e06f47843bbbb7df1e281bd53d29commit hash: 2ad82a1068e1e06f47843bbbb7df1e281bd53d29 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
*/*: 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
commit hash: bbab7f59e9630416397189df70ec133bdd690e38commit hash: bbab7f59e9630416397189df70ec133bdd690e38commit hash: bbab7f59e9630416397189df70ec133bdd690e38commit hash: bbab7f59e9630416397189df70ec133bdd690e38 files touched by this commit
Muhammad Moinur Rahman (bofh) search for other commits by this committer
*/*: 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
commit hash: 620c4e1cad51cfff5d8ebb4b2dafc88d2ede16fdcommit hash: 620c4e1cad51cfff5d8ebb4b2dafc88d2ede16fdcommit hash: 620c4e1cad51cfff5d8ebb4b2dafc88d2ede16fdcommit hash: 620c4e1cad51cfff5d8ebb4b2dafc88d2ede16fd files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
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
commit hash: 6541d6f389c9d95818959222dadbab3d25d8eb08commit hash: 6541d6f389c9d95818959222dadbab3d25d8eb08commit hash: 6541d6f389c9d95818959222dadbab3d25d8eb08commit hash: 6541d6f389c9d95818959222dadbab3d25d8eb08 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/gatk: Update 4.3.0.0 → 4.4.0.0
4.3.0.0
27 Nov 2022 04:06:47
commit hash: dd6279edd58c8afa884e1da75d7621ee706e132dcommit hash: dd6279edd58c8afa884e1da75d7621ee706e132dcommit hash: dd6279edd58c8afa884e1da75d7621ee706e132dcommit hash: dd6279edd58c8afa884e1da75d7621ee706e132d files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/gatk: Update 4.2.6.1 -> 4.3.0.0
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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 View all of this commit message)
4.2.6.1_1
11 Aug 2022 18:33:41
commit hash: b28e6ccdb9656ccd57de05d8dc299647a94b3646commit hash: b28e6ccdb9656ccd57de05d8dc299647a94b3646commit hash: b28e6ccdb9656ccd57de05d8dc299647a94b3646commit hash: b28e6ccdb9656ccd57de05d8dc299647a94b3646 files touched by this commit
Dmitry Marakasov (amdmi3) search for other commits by this committer
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
commit hash: 2c5f8b153e090e52431cd867616f6a58dc73d1a5commit hash: 2c5f8b153e090e52431cd867616f6a58dc73d1a5commit hash: 2c5f8b153e090e52431cd867616f6a58dc73d1a5commit hash: 2c5f8b153e090e52431cd867616f6a58dc73d1a5 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/gatk: Use Java 17 instead of EOLed Java 12
4.2.6.1
23 May 2022 02:05:40
commit hash: 64c437262d4e175501de11a3e855431e8e08833bcommit hash: 64c437262d4e175501de11a3e855431e8e08833bcommit hash: 64c437262d4e175501de11a3e855431e8e08833bcommit hash: 64c437262d4e175501de11a3e855431e8e08833b files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/gatk: Update 4.2.6.0 -> 4.2.6.1
4.2.6.0
10 Apr 2022 23:21:50
commit hash: 0fe062bee9e27456d45d17eb11044d6b406b4b27commit hash: 0fe062bee9e27456d45d17eb11044d6b406b4b27commit hash: 0fe062bee9e27456d45d17eb11044d6b406b4b27commit hash: 0fe062bee9e27456d45d17eb11044d6b406b4b27 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/gatk: Update 4.2.0.0 -> 4.2.6.0
4.2.0.0
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
4.2.0.0
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
4.2.0.0
13 Mar 2021 18:55:15
Revision:568271Original commit files touched by this commit
yuri search for other commits by this committer
biology/gatk: Fix fetch

Reported by:	fallout
4.2.0.0
12 Mar 2021 04:27:49
Revision:568141Original commit files touched by this commit
yuri search for other commits by this committer
biology/gatk: Update 4.1.9.0 -> 4.2.0.0
4.1.9.0_1
22 Jan 2021 02:50:38
Revision:562270Original commit files touched by this commit
yuri search for other commits by this committer
biology/gatk: Add the WITH_LARGE_FILES option.
4.1.9.0
21 Jan 2021 23:15:40
Revision:562258Original commit files touched by this commit
yuri search for other commits by this committer
biology/gatk: Update 4.1.8.1 -> 4.1.9.0
4.1.8.1
08 Sep 2020 19:25:37
Revision:548044Original commit files touched by this commit
yuri search for other commits by this committer
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
Revision:547771Original commit files touched by this commit
yuri search for other commits by this committer
biology/gatk: Update 4.1.8.0 -> 4.1.8.1
4.1.8.0
09 Jul 2020 00:40:56
Revision:541723Original commit files touched by this commit
yuri search for other commits by this committer
biology/gatk: Update 4.1.7.0 -> 4.1.8.0
4.1.7.0
28 May 2020 02:26:52
Revision:536734Original commit files touched by this commit
yuri search for other commits by this committer
biology/gatk: Update 4.1.5.0 -> 4.1.7.0
4.1.5.0
26 May 2020 03:37:48
Revision:536568Original commit files touched by this commit
linimon search for other commits by this committer
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
Revision:534171Original commit files touched by this commit
tobik search for other commits by this committer
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
Revision:527743Original commit files touched by this commit
yuri search for other commits by this committer
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
Revision:525625Original commit files touched by this commit
yuri search for other commits by this committer
biology/gatk: Change from gradle5 to gradle6
4.1.4.1
20 Jan 2020 02:12:37
Revision:523602Original commit files touched by this commit
yuri search for other commits by this committer
biology/gatk: Update 4.1.3.0 -> 4.1.4.1
4.1.3.0
05 Jan 2020 10:33:09
Revision:522133Original commit files touched by this commit
yuri search for other commits by this committer
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
Revision:517997Original commit files touched by this commit
tobik search for other commits by this committer
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
Revision:507364Original commit files touched by this commit
yuri search for other commits by this committer
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
Revision:507197Original commit files touched by this commit
tobik search for other commits by this committer
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
Revision:486619Original commit files touched by this commit
yuri search for other commits by this committer
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
Revision:486561Original commit files touched by this commit
yuri search for other commits by this committer
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
Revision:486503Original commit files touched by this commit
yuri search for other commits by this committer
biology/gatk: Correct the target
4.0.11.0
03 Dec 2018 08:40:53
Revision:486502Original commit files touched by this commit
yuri search for other commits by this committer
New port: biology/gatk: Variant discovery in high-throughput sequencing data

Number of commits found: 34