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Port details
trimmomatic Flexible read trimming tool for Illumina NGS data
0.39 biology on this many watch lists=2 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 0.39Version of this port present on the latest quarterly branch.
There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2016-03-17 08:21:26
Last Update: 2024-04-06 00:12:17
Commit Hash: 2bce913
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
Also Listed In: java
License: GPLv3
WWW:
http://www.usadellab.org/cms/?page=trimmomatic
Description:
Trimmomatic performs a variety of useful trimming tasks for illumina NGS paired-end and single ended data.
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 (14 items)
Collapse this list.
  1. /usr/local/share/licenses/trimmomatic-0.39/catalog.mk
  2. /usr/local/share/licenses/trimmomatic-0.39/LICENSE
  3. /usr/local/share/licenses/trimmomatic-0.39/GPLv3
  4. bin/trimmomatic
  5. share/java/classes/trimmomatic.jar
  6. share/trimmomatic/adapters/NexteraPE-PE.fa
  7. share/trimmomatic/adapters/TruSeq2-PE.fa
  8. share/trimmomatic/adapters/TruSeq2-SE.fa
  9. share/trimmomatic/adapters/TruSeq3-PE-2.fa
  10. share/trimmomatic/adapters/TruSeq3-PE.fa
  11. share/trimmomatic/adapters/TruSeq3-SE.fa
  12. @owner
  13. @group
  14. @mode
Collapse this list.
Dependency lines:
  • trimmomatic>0:biology/trimmomatic
To install the port:
cd /usr/ports/biology/trimmomatic/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/trimmomatic
  • pkg install trimmomatic
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: trimmomatic
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1568469691 SHA256 (Trimmomatic-0.39.zip) = 2f97e3a237378d55c221abfc38e4b11ea232c8a41d511b8b4871f00c0476abca SIZE (Trimmomatic-0.39.zip) = 133596

Packages (timestamps in pop-ups are UTC):
trimmomatic
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest0.390.39-0.390.39---
FreeBSD:13:quarterly0.390.390.390.390.39-0.390.39
FreeBSD:14:latest0.390.390.39-0.39--0.39
FreeBSD:14:quarterly0.390.39--0.39-0.390.39
FreeBSD:15:latest0.390.39n/a-n/a-0.390.39
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Runtime dependencies:
  1. java : java/openjdk8
This port is required by:
for Run
  1. biology/biostar-tools
  2. biology/ddocent

Configuration Options:
No options to configure
Options name:
biology_trimmomatic
USES:
zip
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/
Collapse this list.

Number of commits found: 9

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.39
06 Apr 2024 00:12:17
commit hash: 2bce91331ff30e4e5098a3229eb22f15a4a90dd2commit hash: 2bce91331ff30e4e5098a3229eb22f15a4a90dd2commit hash: 2bce91331ff30e4e5098a3229eb22f15a4a90dd2commit hash: 2bce91331ff30e4e5098a3229eb22f15a4a90dd2 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/trimmomatic: Release to ports@

Focusing on fastq-trim from now on.
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)
0.39
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)
0.39
20 Jul 2022 14:20:57
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.39
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.
0.39
26 Nov 2019 21:46:13
Revision:518482Original commit files touched by this commit
jkim search for other commits by this committer
Clean up after java/openjdk6 and java/openjdk6-jre removal

java/openjdk6 support was removed from Mk/bsd.java.mk (r512662) and
java/openjdk6 and java/openjdk6-jre were removed from the ports tree
(r512663).  Now this patch completely removes remaining stuff from the
ports tree.

PR:			241953 (exp-run)
Reviewed by:		glewis
Approved by:		portmgr (antoine)
Differential Revision:	https://reviews.freebsd.org/D22342
0.39
14 Sep 2019 14:45:49
Revision:512018Original commit files touched by this commit
jwb search for other commits by this committer
biology/trimmomatic: Upgrade to 0.39

Add convenience script to run without knowing the location of the Java jar
0.35
31 Jan 2018 01:07:08
Revision:460452Original commit files touched by this commit
jwb search for other commits by this committer
Multiple ports:
Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org
Remove Created by comments for same user

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14128
0.35
17 Mar 2016 08:21:14
Revision:411261Original commit files touched by this commit
wen search for other commits by this committer
Trimmomatic performs a variety of useful trimming tasks for illumina
NGS paired-end and single ended data.

WWW: http://www.usadellab.org/cms/?page=trimmomatic

PR:		208044
Submitted by:	bacon4000@gmail.com

Number of commits found: 9