GATK, pronounced "Gee Ay Tee Kay" (not "Gat-Kay"), stands for
GenomeAnalysisToolkit. It is a collection of command-line tools for analyzing
high-throughput sequencing data with a primary focus on variant discovery. The
tools can be used individually or chained together into complete workflows.
end-to-end workflows are provided, called GATK Best Practices, tailored for
specific use cases.
Developed in the Data Sciences Platform at the Broad Institute, the toolkit
offers a wide variety of tools with a primary focus on variant discovery and
genotyping. Its powerful processing engine and high-performance computing
features make it capable of taking on projects of any size.
===> The following configuration options are available for gatk-4.7.0.0:
WITH_LARGE_FILES=on: Download large LFS files needed for build and tests
===> Use 'make config' to modify these settings
*/*: Use C.UTF-8 locale
Ports 02f27a83b44d fixed the ports tree to the C locale so it would work
correctly in environments where users use a locale that isn't compatible
with the C locale, e.g. xx_YY.UTF-8 where [A-Z] includes more than just
upper case letters. USE_LOCALE was introduced to let ports use another
locale if they needed it. The C.UTF-8 locale was created later on to be
mostly compatible with the C locale.
Switch the ports tree locale to C.UTF-8 and remove USE_LOCALE. The
world has moved to Unicode so all ports either require it or know how to
build correctly in a Unicode environment.
PR: 295945
Exp-run by: antoine
Mk/**java.mk: Convert bsd.java.mk to USES
The following features have been added or changed:
- Instead of USE_JAVA use USES=java. This defaults to
USES=java:build,run if NO_BUILD is undefined. Else it defaults to
USES=java:run
- Instead of USE_ANT=yes use USES=java:ant which also implies
USES=java:build
- Instead of JAVA_BUILD=yes use USES=java:build. Does not imply run or
extract
- Instead of JAVA_EXTRACT=yes use USES=java:extract does not imply
build or run
- Instead of JAVA_RUN=yes use USES=java:run does not imply extract or
build
- Instead of USE_JAVA=<version> use USES=java and JAVA_VERSION=<version>
Approved by: mat (portmgr), glewis
Differential Revision: https://reviews.freebsd.org/D48201
*/*: 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
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.
(Only the first 15 lines of the commit message are shown above )
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: 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 4.0.11.0 -> 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)
