notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Port details
gatk Variant discovery in high-throughput sequencing data
4.2.0.0 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 4.2.0.0Version 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: 2021-04-07 08:09:01
Commit Hash: cf118cc
Also Listed In: java
License: BSD3CLAUSE
Description:
SVNWeb : git : Homepage
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-4.2.0.0.jar
  3. /usr/local/share/licenses/gatk-4.2.0.0/catalog.mk
  4. /usr/local/share/licenses/gatk-4.2.0.0/LICENSE
  5. /usr/local/share/licenses/gatk-4.2.0.0/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
PKGNAME: gatk
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
gatk
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd644.2.0.04.2.0.0
FreeBSD:11:armv6--
FreeBSD:11:i3864.2.0.04.2.0.0
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd644.2.0.04.2.0.0
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3864.2.0.04.2.0.0
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch644.1.8.1-
FreeBSD:13:amd644.2.0.04.2.0.0
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3864.2.0.04.2.0.0
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64-4.2.0.0
FreeBSD:14:aarch64--
FreeBSD:14:amd644.2.0.0-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3864.2.0.0-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc644.2.0.0-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gradle62 : devel/gradle62
  2. java : java/openjdk8
Runtime dependencies:
  1. java : java/openjdk8
Library dependencies:
  1. libintl.so : devel/gettext-runtime
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/broadinstitute/gatk/tar.gz/4.2.0.0?dummy=/
Collapse this list.

Number of commits found: 23

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  4.2.0.0
mat search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  4.2.0.0
mat search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
13 Mar 2021 18:55:15
Original commit files touched by this commit Revision:568271  4.2.0.0
yuri search for other commits by this committer
biology/gatk: Fix fetch

Reported by:	fallout
12 Mar 2021 04:27:49
Original commit files touched by this commit Revision:568141  4.2.0.0
yuri search for other commits by this committer
biology/gatk: Update 4.1.9.0 -> 4.2.0.0
22 Jan 2021 02:50:38
Original commit files touched by this commit Revision:562270  4.1.9.0_1
yuri search for other commits by this committer
biology/gatk: Add the WITH_LARGE_FILES option.
21 Jan 2021 23:15:40
Original commit files touched by this commit Revision:562258  4.1.9.0
yuri search for other commits by this committer
biology/gatk: Update 4.1.8.1 -> 4.1.9.0
08 Sep 2020 19:25:37
Original commit files touched by this commit Revision:548044  4.1.8.1
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
06 Sep 2020 02:16:45
Original commit files touched by this commit Revision:547771  4.1.8.1
yuri search for other commits by this committer
biology/gatk: Update 4.1.8.0 -> 4.1.8.1
09 Jul 2020 00:40:56
Original commit files touched by this commit Revision:541723  4.1.8.0
yuri search for other commits by this committer
biology/gatk: Update 4.1.7.0 -> 4.1.8.0
28 May 2020 02:26:52
Original commit files touched by this commit Revision:536734  4.1.7.0
yuri search for other commits by this committer
biology/gatk: Update 4.1.5.0 -> 4.1.7.0
26 May 2020 03:37:48
Original commit files touched by this commit Revision:536568  4.1.5.0
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)
06 May 2020 13:11:49
Original commit files touched by this commit Revision:534171  4.1.5.0
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.
04 Mar 2020 08:47:55
Original commit files touched by this commit Revision:527743  4.1.5.0
yuri search for other commits by this committer
biology/gatk: Update 4.1.4.1 -> 4.1.5.0

Reported by:	repology
09 Feb 2020 05:57:04
Original commit files touched by this commit Revision:525625  4.1.4.1_1
yuri search for other commits by this committer
biology/gatk: Change from gradle5 to gradle6
20 Jan 2020 02:12:37
Original commit files touched by this commit Revision:523602  4.1.4.1
yuri search for other commits by this committer
biology/gatk: Update 4.1.3.0 -> 4.1.4.1
05 Jan 2020 10:33:09
Original commit files touched by this commit Revision:522133  4.1.3.0
yuri search for other commits by this committer
biology/gatk: Update 4.1.2.0-43 -> 4.1.3.0

Reported by:	repology
20 Nov 2019 09:51:43
Original commit files touched by this commit Revision:517997  4.1.2.0.43
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
26 Jul 2019 18:03:09
Original commit files touched by this commit Revision:507364  4.1.2.0.43
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
23 Jul 2019 05:28:46
Original commit files touched by this commit Revision:507197  4.0.11.0
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
04 Dec 2018 17:53:46
Original commit files touched by this commit Revision:486619  4.0.11.0
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)
03 Dec 2018 23:04:24
Original commit files touched by this commit Revision:486561  4.0.11.0
yuri search for other commits by this committer
biology/gatk: Change gradle4->gradle because it builds fine with both gradle 4
and 5
03 Dec 2018 08:52:03
Original commit files touched by this commit Revision:486503  4.0.11.0
yuri search for other commits by this committer
biology/gatk: Correct the target
03 Dec 2018 08:40:53
Original commit files touched by this commit Revision:486502  4.0.11.0
yuri search for other commits by this committer
New port: biology/gatk: Variant discovery in high-throughput sequencing data

Number of commits found: 23