| Port details |
- fastq-trim Lightening fast sequence read trimmer
- 0.1.4 biology
 =2      0.1.3_1Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2022-03-19 12:27:08
- Last Update: 2025-04-30 11:11:14
- Commit Hash: b5fed38
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
- License: BSD2CLAUSE
- WWW:
- https://github.com/outpaddling/Fastq-trim
- Description:
- Fastq-trim is a lightening fast read trimming tool for QA of
DNA and RNA reads prior to analyses such as RNA-Seq. it runs
in a fraction of the time required by popular trimmers and uses
only a few megabytes of RAM, so it will run almost entirely in
cache. The design supports adding any number of alignment
functions, so it can be easily adapted to any trimming needs.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- fastq-trim>0:biology/fastq-trim
- To install the port:
- cd /usr/ports/biology/fastq-trim/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/fastq-trim
- pkg install fastq-trim
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: fastq-trim
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1745867331
SHA256 (outpaddling-fastq-trim-0.1.4_GH0.tar.gz) = e31cdccdf0e68f68142917fffaceb9e814b3f217382c2e0f3663a6e1c7a13bb6
SIZE (outpaddling-fastq-trim-0.1.4_GH0.tar.gz) = 29825
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- biolibc>=0.2.6.10 : biology/biolibc
- Library dependencies:
-
- libxtend.so : devel/libxtend
- libbiolibc.so : biology/biolibc
- This port is required by:
- for Run
-
- biology/atac-seq
- biology/chip-seq
- biology/rna-seq
Configuration Options:- No options to configure
- Options name:
- biology_fastq-trim
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 9
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.1.4
30 Apr 2025 11:11:14
 |
Jason W. Bacon (jwb) |
biology/fastq-trim: Update to 0.1.4
Add automatic 5' quality trimming
Changes: https://github.com/auerlab/fastq-trim/releases |
0.1.3_1
02 Mar 2024 19:08:45
|
Nuno Teixeira (eduardo) |
biology/fastq-trim: Move man pages to share/man
Approved by: portmgr (blanket) |
0.1.3
28 Oct 2023 11:34:21
|
Jason W. Bacon (jwb) |
biology/fastq-trim: Update to 0.1.3
fastq-scum: Add zstd and lz4 support
Add low_qual_base_count update for paired end reads
Clean up and expand final output format
A few other minor improvements
Updates for latest libxtend API
Improvements to test script
Changes: https://github.com/auerlab/fastq-trim/releases |
0.1.2
11 Dec 2022 21:24:05
|
Jason W. Bacon (jwb) |
biology/fastq-trim: Update to 0.1.2
Minor enhancements, fixes for SunOS
Changes: https://github.com/auerlab/fastq-trim/releases |
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) |
0.1.1.4
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  ) |
0.1.1.4
21 Mar 2022 21:19:36
|
Jason W. Bacon (jwb) |
biology/fastq-trim: Update to 0.1.1.4
Forgot to update fastq-vis -> fastq-scum in docs in previous update |
0.1.1.2
21 Mar 2022 20:37:43
|
Jason W. Bacon (jwb) |
biology/fastq-trim: Update to 0.1.1.2
Replace crash with run with no arguments with help msg
fastq-vis -> fastq-scum (better name for contamination viewer) |
0.1.1
19 Mar 2022 12:25:58
|
Jason W. Bacon (jwb) |
biology/fastq-trim: Lightening fast sequence read trimmer
Fastq-trim is a lightening fast read trimming tool for QA of
DNA and RNA reads prior to analyses such as RNA-Seq. |
Number of commits found: 9
|
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