| Port details |
- fastp Ultra-fast all-in-one FASTQ preprocessor
- 0.23.4 biology
 =2      0.23.4Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2019-05-03 14:42:13
- Last Update: 2023-05-31 15:40:00
- Commit Hash: 8b9ae52
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: MIT
- WWW:
- https://github.com/OpenGene/fastp
- Description:
- fastp is a tool designed to provide fast all-in-one preprocessing for FastQ
files. This tool is developed in C++ with multithreading supported to afford
high performance.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- To install the port:
- cd /usr/ports/biology/fastp/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/fastp
- pkg install fastp
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: fastp
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1685547158
SHA256 (OpenGene-fastp-v0.23.4_GH0.tar.gz) = 4fad6db156e769d46071add8a778a13a5cb5186bc1e1a5f9b1ffd499d84d72b5
SIZE (OpenGene-fastp-v0.23.4_GH0.tar.gz) = 164071
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:
-
- gmake>=4.3 : devel/gmake
- Library dependencies:
-
- libdeflate.so : archivers/libdeflate
- libisal.so : devel/isa-l
- This port is required by:
- for Run
-
- biology/ddocent
Configuration Options:- No options to configure
- Options name:
- biology_fastp
- USES:
- gmake localbase:ldflags
- 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 |
|---|
0.23.4
31 May 2023 15:40:00
 |
Jason W. Bacon (jwb) |
biology/fastp: Update to 0.23.4
Fix regression in FASTQ reader
Changes: https://github.com/OpenGene/fastp/releases
Reported by: portscout |
0.23.3
14 May 2023 17:10:10
|
Jason W. Bacon (jwb) |
biology/fastp: Update to 0.23.3
Fix hang on bad input and a few other bugs
Changes: https://github.com/OpenGene/fastp/releases
Reported by: portscout |
0.23.2_2
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
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) |
0.23.2_1
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  ) |
0.23.2_1
21 Jan 2022 16:16:01
|
Jason W. Bacon (jwb) |
biology/fastp: Add USE_GCC to hack around seg faults
Upstream has numerous open issues, so it's uncertain if or when the
issue with clang will be resolved. |
0.23.2
30 Dec 2021 16:30:30
|
Jason W. Bacon (jwb) |
biology/fastp: Update to 0.23.2
Interleaved input bug fix |
0.23.1
20 Oct 2021 16:37:39
|
Jason W. Bacon (jwb) |
biology/fastp: Update to 0.23.1
Performance improvements, more reproducible output
Fix seg fault when running with no args |
0.22.0
26 Aug 2021 19:48:10
|
Jason W. Bacon (jwb) |
biology/fastp: Update to 0.22.0
Add support for deduplication |
0.20.1
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.20.1
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.20.1
09 Apr 2020 16:17:03
 |
jwb |
biology/fastp: Upgrade to 0.20.1
Fix the plotly.js CDN issue
Reported by: portscout |
0.20.0_1
26 Jul 2019 20:46:57
|
gerald |
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.
PR: 238330 |
0.20.0
20 May 2019 23:41:09
|
jwb |
biology/fastp: Remove redundant USE_GCC |
0.20.0
04 May 2019 02:07:07
|
jwb |
biology/fastp: Respect WITH_DEBUG - do not strip binary |
0.20.0
03 May 2019 14:41:58
|
jwb |
biology/fastp: Ultra-fast all-in-one FASTQ preprocessor
fastp is a tool designed to provide fast all-in-one preprocessing for FastQ
files. This tool is developed in C++ with multithreading supported to afford
high performance. |
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