notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Want a good monitor light? See my photosAll times are UTC
Ukraine
2024-11-06 Today brought in a new category: filesystems. Sadly, the website did not process it well. I am working on that. It may take a few days.
2024-11-07 Commit processing is halted. I have a fix for the new category. It is making its way through the system.
UPDATE: the backend is processing the original filesystems commit now. It should take about an hour.
UPDATE: as of 20:30 UTC, the filesystems commit has been processed. Commit processing is now up to date.
Port details
readseq Read and reformat biosequences, Java command-line version
2.1.19 biology on this many watch lists=2 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 2.1.19Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-04-18 13:54:12
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
Also Listed In: java
License: PD
WWW:
https://sourceforge.net/projects/readseq
Description:
Sequence reading library developed by the Ribosomal Database Project. It can handle genbank, embl, fasta, fastq, sff and sto files, can read from files or streams, and can handle indexing files.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (5 items)
Collapse this list.
  1. bin/readseq
  2. share/java/classes/readseq.jar
  3. /usr/local/share/licenses/readseq-2.1.19/catalog.mk
  4. /usr/local/share/licenses/readseq-2.1.19/LICENSE
  5. /usr/local/share/licenses/readseq-2.1.19/PD
Collapse this list.
Dependency lines:
  • readseq>0:biology/readseq
To install the port:
cd /usr/ports/biology/readseq/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/readseq
  • pkg install readseq
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: readseq
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1618350447 SHA256 (readseq.jar) = 966e7d4e1c4c6add588b3ead281c993c6a0c35b991a1ded53f81230a54ac6778 SIZE (readseq.jar) = 767702

Packages (timestamps in pop-ups are UTC):
readseq
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.1.192.1.19-2.1.192.1.19---
FreeBSD:13:quarterly2.1.192.1.192.1.192.1.192.1.19-2.1.192.1.19
FreeBSD:14:latest2.1.192.1.192.1.192.1.192.1.19--2.1.19
FreeBSD:14:quarterly2.1.192.1.19-2.1.192.1.19-2.1.192.1.19
FreeBSD:15:latest2.1.192.1.19n/a2.1.19n/a-2.1.192.1.19
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Runtime dependencies:
  1. java : java/openjdk8
This port is required by:
for Run
  1. biology/biostar-tools

Configuration Options:
No options to configure
Options name:
biology_readseq
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://sourceforge.net/projects/readseq/files/latest/
Collapse this list.

Number of commits found: 4

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)
2.1.19
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)
2.1.19
18 Apr 2021 14:20:28
commit hash: 1b6e8568ce41da2e1b99539079b7eba22c8cc013commit hash: 1b6e8568ce41da2e1b99539079b7eba22c8cc013commit hash: 1b6e8568ce41da2e1b99539079b7eba22c8cc013commit hash: 1b6e8568ce41da2e1b99539079b7eba22c8cc013 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/readseq: Remove $FreeBSD$ tag inserted to silence portlint
2.1.19
18 Apr 2021 13:53:02
commit hash: 49a1ada63293e4c27a396fb8997a238dd090e7decommit hash: 49a1ada63293e4c27a396fb8997a238dd090e7decommit hash: 49a1ada63293e4c27a396fb8997a238dd090e7decommit hash: 49a1ada63293e4c27a396fb8997a238dd090e7de files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/readseq: Read and reformat biosequences, Java command-line version

Sequence reading library developed by the Ribosomal Database Project.  It can
handle genbank, embl, fasta, fastq, sff and sto files, can read from files or
streams, and can handle indexing files.

Number of commits found: 4