Picard is a set of command line tools for manipulating high-throughput
sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file
formats are defined in the Hts-specs repository.
Release numerous ports to ports@
I've been retired for a few years, and it is unlikely I will be doing
any more scientific computing support in the future. I have continued
to maintain ~160 ports to the best of my ability, mainly as a favor to
the community, but I can no longer justify the time and effort
required. I am therefore releasing most of my scientific ports, along
with a few others, to ports@. I will continue to maintain ports I am
actively using and those for which I am upstream.
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
*/*: Refactor java/openjdk7 removal
- java/openjdk7* has been removed from the tree since 2022-09-03 however
the relevant codebases in bsd.java.mk has not been removed and the
consumers has also not been updated to use the next jdk version. This
commit updates all relevant consumers to use JAVA_VERSION=8 instead of
JAVA_VERSION=1.7
- Since the introduction of jdk version 18 it looks like similar with
jdk version 8(java version string 1.8). This is prone to error as it
looks similar and is only seperated by a '.'. Remove using
JAVA_VERSION with dotted fomat of java version string and update all
consumers to utilize version 8 instead of 1.8.
Approved by: portmgr (blanket)
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 )
Update CONFLICTS definitions in categories a* to c*
Update the CONFLICTS definitions of ports in the following categories:
- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters
An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.
There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.
Approved by: portmgr (implicit)
biology/picard-tools: CLI tools for manipulating sequencing data
Picard is a set of command line tools for manipulating high-throughput
sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file
formats are defined in the Hts-specs repository.
