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non port: biology/gatk/Makefile

Number of commits found: 31

Monday, 19 Feb 2024
01:48 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)
commit hash: 2ad82a1068e1e06f47843bbbb7df1e281bd53d29 commit hash: 2ad82a1068e1e06f47843bbbb7df1e281bd53d29 commit hash: 2ad82a1068e1e06f47843bbbb7df1e281bd53d29 commit hash: 2ad82a1068e1e06f47843bbbb7df1e281bd53d29 2ad82a1
Sunday, 31 Dec 2023
00:37 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
commit hash: bbab7f59e9630416397189df70ec133bdd690e38 commit hash: bbab7f59e9630416397189df70ec133bdd690e38 commit hash: bbab7f59e9630416397189df70ec133bdd690e38 commit hash: bbab7f59e9630416397189df70ec133bdd690e38 bbab7f5
Monday, 18 Dec 2023
09:14 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
commit hash: 620c4e1cad51cfff5d8ebb4b2dafc88d2ede16fd commit hash: 620c4e1cad51cfff5d8ebb4b2dafc88d2ede16fd commit hash: 620c4e1cad51cfff5d8ebb4b2dafc88d2ede16fd commit hash: 620c4e1cad51cfff5d8ebb4b2dafc88d2ede16fd 620c4e1
Sunday, 4 Jun 2023
22:02 Yuri Victorovich (yuri) search for other commits by this committer
biology/gatk: Update 4.3.0.0 → 4.4.0.0
commit hash: 6541d6f389c9d95818959222dadbab3d25d8eb08 commit hash: 6541d6f389c9d95818959222dadbab3d25d8eb08 commit hash: 6541d6f389c9d95818959222dadbab3d25d8eb08 commit hash: 6541d6f389c9d95818959222dadbab3d25d8eb08 6541d6f
Sunday, 27 Nov 2022
04:06 Yuri Victorovich (yuri) search for other commits by this committer
biology/gatk: Update 4.2.6.1 -> 4.3.0.0
commit hash: dd6279edd58c8afa884e1da75d7621ee706e132d commit hash: dd6279edd58c8afa884e1da75d7621ee706e132d commit hash: dd6279edd58c8afa884e1da75d7621ee706e132d commit hash: dd6279edd58c8afa884e1da75d7621ee706e132d dd6279e
Wednesday, 7 Sep 2022
21:10 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.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 b7f0544
Thursday, 11 Aug 2022
18:33 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
commit hash: b28e6ccdb9656ccd57de05d8dc299647a94b3646 commit hash: b28e6ccdb9656ccd57de05d8dc299647a94b3646 commit hash: b28e6ccdb9656ccd57de05d8dc299647a94b3646 commit hash: b28e6ccdb9656ccd57de05d8dc299647a94b3646 b28e6cc
Tuesday, 24 May 2022
22:39 Yuri Victorovich (yuri) search for other commits by this committer
biology/gatk: Use Java 17 instead of EOLed Java 12
commit hash: 2c5f8b153e090e52431cd867616f6a58dc73d1a5 commit hash: 2c5f8b153e090e52431cd867616f6a58dc73d1a5 commit hash: 2c5f8b153e090e52431cd867616f6a58dc73d1a5 commit hash: 2c5f8b153e090e52431cd867616f6a58dc73d1a5 2c5f8b1
Monday, 23 May 2022
02:05 Yuri Victorovich (yuri) search for other commits by this committer
biology/gatk: Update 4.2.6.0 -> 4.2.6.1
commit hash: 64c437262d4e175501de11a3e855431e8e08833b commit hash: 64c437262d4e175501de11a3e855431e8e08833b commit hash: 64c437262d4e175501de11a3e855431e8e08833b commit hash: 64c437262d4e175501de11a3e855431e8e08833b 64c4372
Sunday, 10 Apr 2022
23:21 Yuri Victorovich (yuri) search for other commits by this committer
biology/gatk: Update 4.2.0.0 -> 4.2.6.0
commit hash: 0fe062bee9e27456d45d17eb11044d6b406b4b27 commit hash: 0fe062bee9e27456d45d17eb11044d6b406b4b27 commit hash: 0fe062bee9e27456d45d17eb11044d6b406b4b27 commit hash: 0fe062bee9e27456d45d17eb11044d6b406b4b27 0fe062b
Wednesday, 7 Apr 2021
08:09 Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c cf118cc
Tuesday, 6 Apr 2021
14:31 Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb 305f148
Friday, 12 Mar 2021
04:27 yuri search for other commits by this committer
biology/gatk: Update 4.1.9.0 -> 4.2.0.0
Original commitRevision:568141 
Friday, 22 Jan 2021
02:50 yuri search for other commits by this committer
biology/gatk: Add the WITH_LARGE_FILES option.
Original commitRevision:562270 
Thursday, 21 Jan 2021
23:15 yuri search for other commits by this committer
biology/gatk: Update 4.1.8.1 -> 4.1.9.0
Original commitRevision:562258 
Sunday, 6 Sep 2020
02:16 yuri search for other commits by this committer
biology/gatk: Update 4.1.8.0 -> 4.1.8.1
Original commitRevision:547771 
Thursday, 9 Jul 2020
00:40 yuri search for other commits by this committer
biology/gatk: Update 4.1.7.0 -> 4.1.8.0
Original commitRevision:541723 
Thursday, 28 May 2020
02:26 yuri search for other commits by this committer
biology/gatk: Update 4.1.5.0 -> 4.1.7.0
Original commitRevision:536734 
Tuesday, 26 May 2020
03:37 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)
Original commitRevision:536568 
Wednesday, 6 May 2020
13:11 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.
Original commitRevision:534171 
Wednesday, 4 Mar 2020
08:47 yuri search for other commits by this committer
biology/gatk: Update 4.1.4.1 -> 4.1.5.0

Reported by:	repology
Original commitRevision:527743 
Sunday, 9 Feb 2020
05:57 yuri search for other commits by this committer
biology/gatk: Change from gradle5 to gradle6
Original commitRevision:525625 
Monday, 20 Jan 2020
02:12 yuri search for other commits by this committer
biology/gatk: Update 4.1.3.0 -> 4.1.4.1
Original commitRevision:523602 
Sunday, 5 Jan 2020
10:33 yuri search for other commits by this committer
biology/gatk: Update 4.1.2.0-43 -> 4.1.3.0

Reported by:	repology
Original commitRevision:522133 
Wednesday, 20 Nov 2019
09:51 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
Original commitRevision:517997 
Friday, 26 Jul 2019
18:03 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
Original commitRevision:507364 
Tuesday, 23 Jul 2019
05:28 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
Original commitRevision:507197 
Tuesday, 4 Dec 2018
17:53 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)
Original commitRevision:486619 
Monday, 3 Dec 2018
23:04 yuri search for other commits by this committer
biology/gatk: Change gradle4->gradle because it builds fine with both gradle 4
and 5
Original commitRevision:486561 
08:52 yuri search for other commits by this committer
biology/gatk: Correct the target
Original commitRevision:486503 
08:40 yuri search for other commits by this committer
New port: biology/gatk: Variant discovery in high-throughput sequencing data
Original commitRevision:486502 

Number of commits found: 31