biology/gatk: Update COMMENT

biology/gatk: Add dependencies biology/fermi-lite and biology/gkl; Add python
dependency for tests

biology/gatk: Fix fetch

biology/gatk: Fix fetch

Reported by:	fallout

biology/gatk: Prevent execution of git hooks from $DISTDIR during fetch

biology/gatk: update 4.5.0.0 → 4.6.0.0

*/*: 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)

*/*: 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

biology/gatk: update 4.4.0.0 → 4.5.0.0

ChangeLog: https://github.com/broadinstitute/gatk/releases/tag/4.5.0.0

biology/gatk: Update 4.3.0.0 → 4.4.0.0

biology/gatk: Update 4.2.6.1 -> 4.3.0.0

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)

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.

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

biology/gatk: Use Java 17 instead of EOLed Java 12

biology/gatk: Update 4.2.6.0 -> 4.2.6.1

biology/gatk: Update 4.2.0.0 -> 4.2.6.0

One more small cleanup, forgotten yesterday.
Reported by:	lwhsu

Remove # $FreeBSD$ from Makefiles.

biology/gatk: Fix fetch

Reported by:	fallout

biology/gatk: Update 4.1.9.0 -> 4.2.0.0

biology/gatk: Add the WITH_LARGE_FILES option.

biology/gatk: Update 4.1.8.1 -> 4.1.9.0

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

biology/gatk: Update 4.1.8.0 -> 4.1.8.1

biology/gatk: Update 4.1.7.0 -> 4.1.8.0

biology/gatk: Update 4.1.5.0 -> 4.1.7.0

Mark as BROKEN on powerpc64 12.  It builds on -head.

While here, pet portlint (remove extra blank line).

Approved by:	portmgr (tier-2 blanket)

Preserve Gradle 6.2.2 for biology/gatk

It fails to build with newer Gradle versions again.

biology/gatk: Update 4.1.4.1 -> 4.1.5.0

Reported by:	repology

biology/gatk: Change from gradle5 to gradle6

biology/gatk: Update 4.1.3.0 -> 4.1.4.1

biology/gatk: Update 4.1.2.0-43 -> 4.1.3.0

Reported by:	repology

Create devel/gradle5 in preparation of devel/gradle update

Many consumers fail to build with newer Gradle versions.

PR:		239875, 239900, 239901, 239902

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

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

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)

biology/gatk: Change gradle4->gradle because it builds fine with both gradle 4
and 5

biology/gatk: Correct the target

New port: biology/gatk: Variant discovery in high-throughput sequencing data