| Port details |
- p5-TrimGalore Wrapper around Cutadapt and FastQC for adapter and quality trimming
- 0.6.10 biology
 =2      0.6.5Version 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
- Port Added: 2017-12-09 13:23:40
- Last Update: 2024-07-23 15:01:28
- Commit Hash: 18b2a58
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: perl5 python
- License: GPLv3
- WWW:
- https://github.com/FelixKrueger/TrimGalore
- Description:
- Wrapper around Cutadapt and FastQC to consistently apply adapter and quality
trimming to FastQ files, with extra functionality for RRBS data.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- p5-TrimGalore>0:biology/p5-TrimGalore
- To install the port:
- cd /usr/ports/biology/p5-TrimGalore/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/p5-TrimGalore
- pkg install p5-TrimGalore
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: p5-TrimGalore
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1721746682
SHA256 (FelixKrueger-TrimGalore-0.6.10_GH0.tar.gz) = 3a4e414fc658d6eb4356f1572351204e8475a9d7dc79f6798270b57d35bda017
SIZE (FelixKrueger-TrimGalore-0.6.10_GH0.tar.gz) = 26831358
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:
-
- py311-cutadapt>=2.5 : biology/py-cutadapt@py311
- fastqc>0 : biology/fastqc
- perl5>=5.36<5.37 : lang/perl5.36
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_p5-TrimGalore
- USES:
- perl5 python:env shebangfix
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.6.10
23 Jul 2024 15:01:28
 |
Neel Chauhan (nc) |
biology/p5-TrimGalore: Update to 0.6.10 |
0.6.5
06 Apr 2024 00:12:17
|
Jason W. Bacon (jwb) |
biology/p5-TrimGalore: Release to ports@
Focusing on fastq-trim from now on. |
0.6.5
05 Aug 2023 20:05:05
|
Muhammad Moinur Rahman (bofh) |
biology/p5-TrimGalore: Fix build
LICENSE had a typo.
Approved by: portmgr (blanket)
Sponsored by: The FreeBSD Foundation |
0.6.5
27 Jun 2023 19:34:34
|
Rene Ladan (rene) |
all: remove explicit versions in USES=python for "3.x+"
The logic in USES=python will automatically convert this to 3.8+ by
itself.
Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.
finance/quickfix: mark BROKEN with PYTHON
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
^~~~~~~~~~
1 warning and 1 error generated.
Reviewed by: portmgr, vishwin, yuri
Differential Revision: <https://reviews.freebsd.org/D40568> |
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) |
0.6.5
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  ) |
0.6.5
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.6.5
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.6.5
26 Nov 2019 16:20:12
 |
jwb |
biology/p5-TrimGalore: Upgrade to 0.6.5
Minor bugfixes and enhancements
Reported by: portscout |
0.6.4
21 Sep 2019 02:51:26
|
jwb |
biology/p5-TrimGalore: Upgrade to 0.6.4
Improved adapter autodetection, minor bug fixes. |
0.6.1
24 Mar 2019 21:44:17
|
jwb |
biology/p5-TrimGalore: Upgrade to 0.6.1
Add test script |
0.4.5
24 Mar 2019 20:28:55
|
antoine |
Unbreak |
0.4.5
09 Dec 2017 13:23:32
|
jwb |
[new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adapter
and quality trimming
Approved by: jrm (mentor)
Differential Revision: D13400 |
As an Amazon Associate I earn from qualifying purchases.