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Port details
fastx-toolkit CLI tools for Short-Reads FASTA/FASTQ files preprocessing
0.0.14 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 Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2015-09-25 18:33:28
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
License: AGPLv3+
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
pkg-plist: as obtained via: make generate-plist
Expand this list (29 items)
Collapse this list.
  1. /usr/local/share/licenses/fastx_toolkit-0.0.14/catalog.mk
  2. /usr/local/share/licenses/fastx_toolkit-0.0.14/LICENSE
  3. /usr/local/share/licenses/fastx_toolkit-0.0.14/AGPLv3+
  4. bin/fasta_clipping_histogram.pl
  5. bin/fasta_formatter
  6. bin/fasta_nucleotide_changer
  7. bin/fastq_masker
  8. bin/fastq_quality_boxplot_graph.sh
  9. bin/fastq_quality_converter
  10. bin/fastq_quality_filter
  11. bin/fastq_quality_trimmer
  12. bin/fastq_to_fasta
  13. bin/fastx_artifacts_filter
  14. bin/fastx_barcode_splitter.pl
  15. bin/fastx_clipper
  16. bin/fastx_collapser
  17. bin/fastx_nucleotide_distribution_graph.sh
  18. bin/fastx_nucleotide_distribution_line_graph.sh
  19. bin/fastx_quality_stats
  20. bin/fastx_renamer
  21. bin/fastx_reverse_complement
  22. bin/fastx_trimmer
  23. bin/fastx_uncollapser
  24. share/aclocal/ax_c_long_long.m4
  25. share/aclocal/ax_cxx_compile_stdcxx_11.m4
  26. share/aclocal/ax_cxx_header_stdcxx_tr1.m4
  27. @owner
  28. @group
  29. @mode
Collapse this list.
Dependency lines:
  • fastx_toolkit>0:biology/fastx-toolkit
Conflicts:
CONFLICTS_INSTALL:
  • autoconf-archive
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
To install the port:
cd /usr/ports/biology/fastx-toolkit/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/fastx-toolkit
  • pkg install fastx_toolkit
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: fastx_toolkit
Flavors: there is no flavor information for this port.
distinfo:

Packages (timestamps in pop-ups are UTC):
fastx_toolkit
ABIlatestquarterly
FreeBSD:11:aarch640.0.140.0.14
FreeBSD:11:amd640.0.140.0.14
FreeBSD:11:armv60.0.140.0.14
FreeBSD:11:i3860.0.140.0.14
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips640.0.140.0.14
FreeBSD:12:aarch640.0.140.0.14
FreeBSD:12:amd640.0.140.0.14
FreeBSD:12:armv60.0.140.0.14
FreeBSD:12:armv70.0.140.0.14
FreeBSD:12:i3860.0.140.0.14
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips640.0.140.0.14
FreeBSD:12:powerpc64pkg-fallout0.0.14
FreeBSD:13:aarch640.0.140.0.14
FreeBSD:13:amd640.0.140.0.14
FreeBSD:13:armv60.0.140.0.14
FreeBSD:13:armv70.0.140.0.14
FreeBSD:13:i3860.0.140.0.14
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips640.0.140.0.14
FreeBSD:13:powerpc640.0.140.0.14
FreeBSD:13:riscv64pkg-fallout0.0.14
FreeBSD:14:aarch640.0.14pkg-fallout
FreeBSD:14:amd640.0.14pkg-fallout
FreeBSD:14:armv60.0.14pkg-fallout
FreeBSD:14:armv70.0.14pkg-fallout
FreeBSD:14:i3860.0.14pkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips640.0.14pkg-fallout
FreeBSD:14:powerpc640.0.14pkg-fallout
FreeBSD:14:riscv640.0.14pkg-fallout
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. pkgconf>=1.3.0_1 : devel/pkgconf
  2. autoconf>=2.71 : devel/autoconf
  3. automake>=1.16.5 : devel/automake
  4. libtoolize : devel/libtool
Runtime dependencies:
  1. perl5>=5.32.r0<5.33 : lang/perl5.32
Library dependencies:
  1. libgtextutils.so : biology/libgtextutils
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message

Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/agordon/fastx_toolkit/tar.gz/0.0.14?dummy=/
Collapse this list.

Number of commits found: 13

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
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)
0.0.14
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)
0.0.14
06 Feb 2022 18:36:07
commit hash:bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash:bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash:bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash:bdd2d4af9630fdc1157d49bd193e8195c3240e9e files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Update CONFLICTS definitions in categories a* to c*

Update the CONFLICTS definitions of ports in the following categories:

- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters

An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.

There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.

Approved by:	portmgr (implicit)
0.0.14
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
0.0.14
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.
0.0.14
16 May 2018 15:13:43
Revision:470124Original commit files touched by this commit
jwb search for other commits by this committer
biology/fastx-toolkit: Fix build on FreeBSD 12

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15451
0.0.14
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
0.0.14
01 Apr 2016 13:29:17
Revision:412344Original commit files touched by this commit
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
0.0.14
24 Mar 2016 14:12:23
Revision:411790Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Clarify LICENSE
- Add LICENSE_FILE
- Remove USES=tar:bzip2 (incorrect and no-op with USE_GITHUB)
- Drop unneeded (and incorrect anyway) PKG_CONFIG_PATH

Approved by:	portmgr blanket
0.0.14
08 Mar 2016 13:09:12
Revision:410613Original commit files touched by this commit
mat search for other commits by this committer
Always set the DEFAULT github DISTFILE with .tar.gz for EXTRACT_SUFX.

Fix distinfo for the offending ports.

lang/yorick's tag was moved, and the added patch was no longer needed.

PR:			207644
Submitted by:		mat
Exp-run by by:		antoine
Sponsored by:		Absolight
Differential Revision:	https://reviews.freebsd.org/D4268
0.0.14
29 Dec 2015 14:30:47
Revision:404743Original commit files touched by this commit
mat search for other commits by this committer
Cleanup GH_* and variables order.

Sponsored by:	Absolight
0.0.14
11 Dec 2015 08:48:57
Revision:403506Original commit files touched by this commit
miwi search for other commits by this committer
- Update maintainer mail address
- Update/Remove MASTER_SITE

PR:		204755
Submitted by:	 jwbacon@tds.net (maintainer)
Approved by:	mat (mentor)
Differential Revision:	D4493
0.0.14
25 Sep 2015 18:33:18
Revision:397847Original commit files touched by this commit
rm search for other commits by this committer
The FASTX-Toolkit is a collection of command line tools for Short-Reads
FASTA/FASTQ files preprocessing.

WWW: http://hannonlab.cshl.edu/fastx_toolkit/

PR:		203318
Submitted by:	Jason Bacon <jwbacon@tds.net>

Number of commits found: 13