FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and
protein sequences. Common manipulations of FASTA/Q file include converting,
searching, filtering, deduplication, splitting, shuffling, and sampling.
Existing tools only implement some of these manipulations, and not particularly
efficiently, and some are only available for certain operating systems.
Furthermore, the complicated installation process of required packages and
running environments can render these programs less user friendly.
SeqKit is a cross-platform ultrafast comprehensive toolkit for FASTA/Q
processing. SeqKit provides executable binary files for all major operating
systems, including Windows, Linux, and Mac OS X, and can be directly used
without any dependencies or pre-configurations. SeqKit demonstrates competitive
performance in execution time and memory usage compared to similar tools. The
efficiency and usability of SeqKit enable researchers to rapidly accomplish
common FASTA/Q file manipulations.
many: Unpin Go ports
* Ports that were pinned to a deprecated version of Go (1.23 or older)
have been unpinned.
* Ports that were pinned to a still-supported version of Go (1.24 or
newer) have been converted to requesting that as their minimum Go
version.
* Ports that had been forcibly deprecated for pinning an expired Go
version have been undeprecated.
go: Bump go124-dependent ports
Earlier I bumped the default Go to 1.24. Ports that specify a lower
version will still build with those lower version (for now), so they
don't need a bumping. Instead I'm bumping anything that (now) has go124
as a dependency.
biology/seqkit: fix build on riscv64
Bump golang.org/x/sys dependency to a version new enough
to support riscv64-freebsd.
Sponsored by: Berliner Linux User Group e.V.
Approved by: yuri (maintainer)
Differential Revision: https://reviews.freebsd.org/D39154
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)
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 )
