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Port details
gatk Variant discovery in high-throughput sequencing data
4.1.4.1 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 4.1.2.0.43Version 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: 2020-01-20 02:12:37
SVN Revision: 523602
Also Listed In: java
License: BSD3CLAUSE
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (5 items)
  1. bin/gatk
  2. /usr/local/share/java/classes/GenomeAnalysisTK-4.1.4.1.jar
  3. /usr/local/share/licenses/gatk-4.1.4.1/catalog.mk
  4. /usr/local/share/licenses/gatk-4.1.4.1/LICENSE
  5. /usr/local/share/licenses/gatk-4.1.4.1/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: pkg install gatk
PKGNAME: gatk
Flavors: there is no flavor information for this port.
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gradle5 : devel/gradle5
  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

USES:

Master Sites:
  1. https://codeload.github.com/broadinstitute/gatk/tar.gz/4.1.4.1?dummy=/

Number of commits found: 9

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
20 Jan 2020 02:12:37
Original commit files touched by this commit  4.1.4.1
Revision:523602
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  4.1.3.0
Revision:522133
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  4.1.2.0.43
Revision:517997
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  4.1.2.0.43
Revision:507364
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  4.0.11.0
Revision:507197
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  4.0.11.0
Revision:486619
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  4.0.11.0
Revision:486561
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  4.0.11.0
Revision:486503
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  4.0.11.0
Revision:486502
yuri search for other commits by this committer
New port: biology/gatk: Variant discovery in high-throughput sequencing data

Number of commits found: 9

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