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A new feature has been added. FreshPorts already tracks package built by the FreeBSD project. This information is displayed on each port page. You can now get an email when FreshPorts notices a new package is available for something on one of your watch lists. However, you must opt into that. Click on Report Subscriptions on the right, and New Package Notification box, and click on Update.

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Port details
fastp Ultra-fast all-in-one FASTQ preprocessor
0.23.4 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 0.23.4Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-05-03 14:42:13
Last Update: 2023-05-31 15:40:00
Commit Hash: 8b9ae52
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.
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 (4 items)
Collapse this list.
  1. bin/fastp
  2. /usr/local/share/licenses/fastp-0.23.4/catalog.mk
  3. /usr/local/share/licenses/fastp-0.23.4/LICENSE
  4. /usr/local/share/licenses/fastp-0.23.4/MIT
Collapse this list.
Dependency lines:
  • fastp>0:biology/fastp
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):
fastp
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest-0.23.40.20.1---0.20.1-
FreeBSD:13:quarterly-0.23.4---0.23.40.23.40.23.4
FreeBSD:14:latest-0.23.4---0.23.4-0.23.4
FreeBSD:14:quarterly-0.23.4---0.23.40.23.40.23.4
FreeBSD:15:latest-0.23.4n/a-n/a0.23.40.23.40.23.4
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
Library dependencies:
  1. libdeflate.so : archivers/libdeflate
  2. libisal.so : devel/isa-l
This port is required by:
for Run
  1. 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:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/OpenGene/fastp/tar.gz/v0.23.4?dummy=/
Collapse this list.

Number of commits found: 16

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.23.4
31 May 2023 15:40:00
commit hash: 8b9ae52ebb8c82a291c64a86a02607ccf3337737commit hash: 8b9ae52ebb8c82a291c64a86a02607ccf3337737commit hash: 8b9ae52ebb8c82a291c64a86a02607ccf3337737commit hash: 8b9ae52ebb8c82a291c64a86a02607ccf3337737 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
commit hash: 4d258e203e82516725e3b1c3f96a531572265861commit hash: 4d258e203e82516725e3b1c3f96a531572265861commit hash: 4d258e203e82516725e3b1c3f96a531572265861commit hash: 4d258e203e82516725e3b1c3f96a531572265861 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b files touched by this commit
Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
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)
0.23.2_1
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)
0.23.2_1
21 Jan 2022 16:16:01
commit hash: 265238ee6c37a6abc5ad035a20d91f505d125394commit hash: 265238ee6c37a6abc5ad035a20d91f505d125394commit hash: 265238ee6c37a6abc5ad035a20d91f505d125394commit hash: 265238ee6c37a6abc5ad035a20d91f505d125394 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
commit hash: 082c7a0de2386500145ed64a2a596ec523999f12commit hash: 082c7a0de2386500145ed64a2a596ec523999f12commit hash: 082c7a0de2386500145ed64a2a596ec523999f12commit hash: 082c7a0de2386500145ed64a2a596ec523999f12 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/fastp: Update to 0.23.2

Interleaved input bug fix
0.23.1
20 Oct 2021 16:37:39
commit hash: f6c6c5a37954173f208f39515fdf79d1dc6e2689commit hash: f6c6c5a37954173f208f39515fdf79d1dc6e2689commit hash: f6c6c5a37954173f208f39515fdf79d1dc6e2689commit hash: f6c6c5a37954173f208f39515fdf79d1dc6e2689 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
commit hash: 7813a6f1a1648f0ae7db14dddf575dd84bea11cccommit hash: 7813a6f1a1648f0ae7db14dddf575dd84bea11cccommit hash: 7813a6f1a1648f0ae7db14dddf575dd84bea11cccommit hash: 7813a6f1a1648f0ae7db14dddf575dd84bea11cc files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/fastp: Update to 0.22.0

Add support for deduplication
0.20.1
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
0.20.1
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.
0.20.1
09 Apr 2020 16:17:03
Revision:531215Original commit files touched by this commit
jwb search for other commits by this committer
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
Revision:507372Original commit files touched by this commit
gerald search for other commits by this committer
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
Revision:502178Original commit files touched by this commit
jwb search for other commits by this committer
biology/fastp: Remove redundant USE_GCC
0.20.0
04 May 2019 02:07:07
Revision:500770Original commit files touched by this commit
jwb search for other commits by this committer
biology/fastp: Respect WITH_DEBUG - do not strip binary
0.20.0
03 May 2019 14:41:58
Revision:500737Original commit files touched by this commit
jwb search for other commits by this committer
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.

Number of commits found: 16