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Port details
picard-tools CLI tools for manipulating high-throughput sequencing (HTS) data
2.22.9 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.22.9Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2020-06-13 13:54:53
Last Update: 2023-04-04 18:10:53
Commit Hash: 4cda17a
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (5 items)
Collapse this list.
  1. bin/picard
  2. /usr/local/share/java/classes/picard.jar
  3. /usr/local/share/licenses/picard-tools-2.22.9/catalog.mk
  4. /usr/local/share/licenses/picard-tools-2.22.9/LICENSE
  5. /usr/local/share/licenses/picard-tools-2.22.9/MIT
Collapse this list.
Dependency lines:
  • picard-tools>0:biology/picard-tools
Conflicts:
CONFLICTS_INSTALL:
  • picard
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
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):
picard-tools
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.22.92.22.9-2.22.92.22.9---
FreeBSD:13:quarterly2.22.92.22.92.22.92.22.92.22.9-2.22.92.22.9
FreeBSD:14:latest2.22.92.22.92.22.9-2.22.9--2.22.9
FreeBSD:14:quarterly2.22.92.22.9--2.22.9-2.22.92.22.9
FreeBSD:15:latest2.22.92.22.9n/a-n/a-2.22.92.22.9
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Runtime dependencies:
  1. samtools : biology/samtools
  2. java : java/openjdk8
This port is required by:
for Run
  1. 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:
Expand this list (1 items)
Collapse this list.
  1. http://github.com/broadinstitute/picard/releases/download/2.22.9/
Collapse this list.

Number of commits found: 8

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.22.9
04 Apr 2023 18:10:53
commit hash: 4cda17ab14588e6e4fdac7f697e246554ce82af3commit hash: 4cda17ab14588e6e4fdac7f697e246554ce82af3commit hash: 4cda17ab14588e6e4fdac7f697e246554ce82af3commit hash: 4cda17ab14588e6e4fdac7f697e246554ce82af3 files touched by this commit
Muhammad Moinur Rahman (bofh) search for other commits by this committer
*/*: 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
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
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.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.22.9
06 Feb 2022 18:36:07
commit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9e files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
2.22.9
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
2.22.9
30 Aug 2020 14:06:54
Revision:547056Original commit files touched by this commit
jwb search for other commits by this committer
biology/picard-tools: Remove extraneous file

Reported by:    Roman Bogorodskiy
2.22.9
13 Jun 2020 13:54:47
Revision:538672Original commit files touched by this commit
jwb search for other commits by this committer
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