non port: biology/gatk/Makefile |
Number of commits found: 31 |
Monday, 19 Feb 2024
|
01:48 Yuri Victorovich (yuri)
*/*: 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)
2ad82a1 |
Sunday, 31 Dec 2023
|
00:37 Muhammad Moinur Rahman (bofh)
*/*: 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
bbab7f5 |
Monday, 18 Dec 2023
|
09:14 Yuri Victorovich (yuri)
biology/gatk: update 4.4.0.0 → 4.5.0.0
ChangeLog: https://github.com/broadinstitute/gatk/releases/tag/4.5.0.0
620c4e1 |
Sunday, 4 Jun 2023
|
22:02 Yuri Victorovich (yuri)
biology/gatk: Update 4.3.0.0 → 4.4.0.0
6541d6f |
Sunday, 27 Nov 2022
|
04:06 Yuri Victorovich (yuri)
biology/gatk: Update 4.2.6.1 -> 4.3.0.0
dd6279e |
Wednesday, 7 Sep 2022
|
21:10 Stefan Eßer (se)
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)
b7f0544 |
Thursday, 11 Aug 2022
|
18:33 Dmitry Marakasov (amdmi3)
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
b28e6cc |
Tuesday, 24 May 2022
|
22:39 Yuri Victorovich (yuri)
biology/gatk: Use Java 17 instead of EOLed Java 12
2c5f8b1 |
Monday, 23 May 2022
|
02:05 Yuri Victorovich (yuri)
biology/gatk: Update 4.2.6.0 -> 4.2.6.1
64c4372 |
Sunday, 10 Apr 2022
|
23:21 Yuri Victorovich (yuri)
biology/gatk: Update 4.2.0.0 -> 4.2.6.0
0fe062b |
Wednesday, 7 Apr 2021
|
08:09 Mathieu Arnold (mat)
One more small cleanup, forgotten yesterday.
Reported by: lwhsu
cf118cc |
Tuesday, 6 Apr 2021
|
14:31 Mathieu Arnold (mat)
Remove # $FreeBSD$ from Makefiles.
305f148 |
Friday, 12 Mar 2021
|
04:27 yuri
biology/gatk: Update 4.1.9.0 -> 4.2.0.0
|
Friday, 22 Jan 2021
|
02:50 yuri
biology/gatk: Add the WITH_LARGE_FILES option.
|
Thursday, 21 Jan 2021
|
23:15 yuri
biology/gatk: Update 4.1.8.1 -> 4.1.9.0
|
Sunday, 6 Sep 2020
|
02:16 yuri
biology/gatk: Update 4.1.8.0 -> 4.1.8.1
|
Thursday, 9 Jul 2020
|
00:40 yuri
biology/gatk: Update 4.1.7.0 -> 4.1.8.0
|
Thursday, 28 May 2020
|
02:26 yuri
biology/gatk: Update 4.1.5.0 -> 4.1.7.0
|
Tuesday, 26 May 2020
|
03:37 linimon
Mark as BROKEN on powerpc64 12. It builds on -head.
While here, pet portlint (remove extra blank line).
Approved by: portmgr (tier-2 blanket)
|
Wednesday, 6 May 2020
|
13:11 tobik
Preserve Gradle 6.2.2 for biology/gatk
It fails to build with newer Gradle versions again.
|
Wednesday, 4 Mar 2020
|
08:47 yuri
biology/gatk: Update 4.1.4.1 -> 4.1.5.0
Reported by: repology
|
Sunday, 9 Feb 2020
|
05:57 yuri
biology/gatk: Change from gradle5 to gradle6
|
Monday, 20 Jan 2020
|
02:12 yuri
biology/gatk: Update 4.1.3.0 -> 4.1.4.1
|
Sunday, 5 Jan 2020
|
10:33 yuri
biology/gatk: Update 4.1.2.0-43 -> 4.1.3.0
Reported by: repology
|
Wednesday, 20 Nov 2019
|
09:51 tobik
Create devel/gradle5 in preparation of devel/gradle update
Many consumers fail to build with newer Gradle versions.
PR: 239875, 239900, 239901, 239902
|
Friday, 26 Jul 2019
|
18:03 yuri
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
|
Tuesday, 23 Jul 2019
|
05:28 tobik
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
|
Tuesday, 4 Dec 2018
|
17:53 yuri
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)
|
Monday, 3 Dec 2018
|
23:04 yuri
biology/gatk: Change gradle4->gradle because it builds fine with both gradle 4
and 5
|
08:52 yuri
biology/gatk: Correct the target
|
08:40 yuri
New port: biology/gatk: Variant discovery in high-throughput sequencing data
|
Number of commits found: 31 |