| Port details |
- picard-tools CLI tools for manipulating high-throughput sequencing (HTS) data
- 2.22.9 biology
 =2      2.22.9Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2020-06-13 13:54:53
- Last Update: 2023-04-04 18:10:53
- Commit Hash: 4cda17a
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: java
- License: MIT
- WWW:
- https://broadinstitute.github.io/picard/
- Description:
- 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.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- picard-tools>0:biology/picard-tools
- Conflicts:
- CONFLICTS_INSTALL:
- To install the port:
- cd /usr/ports/biology/picard-tools/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/picard-tools
- pkg install picard-tools
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: picard-tools
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1591387929
SHA256 (picard.jar) = a3d8830f68443a745cca9e1bab9adbc1c435fe3639709b118f5a89858a12a362
SIZE (picard.jar) = 17520128
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Runtime dependencies:
-
- samtools : biology/samtools
- java : java/openjdk8
- This port is required by:
- for Run
-
- biology/biostar-tools
Configuration Options:- No options to configure
- Options name:
- biology_picard-tools
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 8
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
2.22.9
04 Apr 2023 18:10:53
 |
Muhammad Moinur Rahman (bofh) |
*/*: 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) |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
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) |
2.22.9
07 Sep 2022 21:10:59
|
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.
(Only the first 15 lines of the commit message are shown above  ) |
2.22.9
06 Feb 2022 18:36:07
|
Stefan Eßer (se) |
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) |
2.22.9
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.22.9
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.22.9
30 Aug 2020 14:06:54
 |
jwb |
biology/picard-tools: Remove extraneous file
Reported by: Roman Bogorodskiy |
2.22.9
13 Jun 2020 13:54:47
|
jwb |
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. |
Number of commits found: 8
|
As an Amazon Associate I earn from qualifying purchases.