notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Ukraine
NOTE: the WWW: line in pkg-descr was relocated to a WWW= line in Makefile. Each port in FreshPorts has a homepage link. Look for it right after the Description: on each port's home page.

Do I know someone who can pick up a server from 7401 E. Ben White Blvd. Austin TX?

The emphasis is on know, or recommended by someone I know. This is the original FreshPorts server, way past useful: RAID, 8GB RAM, etc. The drives need to be wiped and everything recycled.
Port details
gatk Variant discovery in high-throughput sequencing data
4.2.6.1_1 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 Version of this port present on the latest quarterly branch.
Broken BROKEN: fails to build: Build failed with an exception
Ignore IGNORE: is marked as broken: fails to build: Build failed with an exception
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-12-03 08:41:01
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
Also Listed In: java
License: BSD3CLAUSE
Description:
HomepagecgitgithubgitlabSVNWeb
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-4.2.6.1.jar
  3. /usr/local/share/licenses/gatk-4.2.6.1_1/catalog.mk
  4. /usr/local/share/licenses/gatk-4.2.6.1_1/LICENSE
  5. /usr/local/share/licenses/gatk-4.2.6.1_1/BSD3CLAUSE
Collapse this list.
Dependency lines:
  • gatk>0:biology/gatk
To install the port:
cd /usr/ports/biology/gatk/ && make install clean
A package is not available for ports marked as:
Forbidden / Broken / Ignore / Restricted
PKGNAME: gatk
Flavors: there is no flavor information for this port.
distinfo:

Packages (timestamps in pop-ups are UTC):
gatk
ABIlatestquarterly
FreeBSD:11:aarch64pkg-falloutpkg-fallout
FreeBSD:11:amd644.2.0.04.2.0.0
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i3864.2.0.04.2.0.0
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-falloutpkg-fallout
FreeBSD:12:amd64pkg-fallout4.2.6.1_1
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i386pkg-fallout4.2.6.1_1
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch64pkg-falloutpkg-fallout
FreeBSD:13:amd64pkg-fallout4.2.6.1_1
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i386pkg-fallout4.2.6.1_1
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-fallout4.2.0.0
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch64pkg-falloutpkg-fallout
FreeBSD:14:amd64pkg-falloutpkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i386pkg-falloutpkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc644.2.0.0pkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 

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
Runtime dependencies:
  1. java : java/openjdk17
Library dependencies:
  1. libintl.so : devel/gettext-runtime
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

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/4.2.6.1?dummy=/
Collapse this list.

Number of commits found: 29

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit 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: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: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: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: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: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: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: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: 29