FreshPorts -- biology/rubygem-bio: Integrated environment for Bioinformatics written in Ruby

Port details

rubygem-bio Integrated environment for Bioinformatics written in Ruby

2.0.6 biology =2 2.0.5Version of this port present on the latest quarterly branch.

Maintainer: ruby@FreeBSD.org

Port Added: 2017-02-05 04:27:03

Last Update: 2025-03-19 03:46:26

Commit Hash: b9c852a

People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane

Also Listed In: rubygems

License: BSD2CLAUSE RUBY

WWW:

http://bioruby.org/

Description:

BioRuby project aims to implement integrated environment for Bioinformatics by using Ruby.

¦ ¦ ¦ ¦

Manual pages:

FreshPorts has no man page information for this port.

pkg-plist: as obtained via: make generate-plist

Expand this list (4 items)

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/usr/local/share/licenses/rubygem-bio-2.0.6/catalog.mk
/usr/local/share/licenses/rubygem-bio-2.0.6/LICENSE
/usr/local/share/licenses/rubygem-bio-2.0.6/BSD2CLAUSE
/usr/local/share/licenses/rubygem-bio-2.0.6/RUBY

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Dependency lines:

rubygem-bio>0:biology/rubygem-bio

To install the port:

cd /usr/ports/biology/rubygem-bio/ && make install clean

To add the package, run one of these commands:

pkg install biology/rubygem-bio
pkg install rubygem-bio

NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.

PKGNAME: rubygem-bio

Flavors: there is no flavor information for this port.

distinfo:

TIMESTAMP = 1742070824 SHA256 (rubygem/bio-2.0.6.gem) = e2c39b0c30967457b9b636ede3e567b00ec06ca1752b7d27135b7b2762df05f1 SIZE (rubygem/bio-2.0.6.gem) = 1424384

Packages (timestamps in pop-ups are UTC):

rubygem-bio
ABI	aarch64	amd64	armv6	armv7	i386	powerpc	powerpc64	powerpc64le
FreeBSD:13:latest	2.0.5	2.0.6	2.0.1	2.0.5	2.0.6	-	2.0.1	-
FreeBSD:13:quarterly	2.0.5	2.0.5	2.0.4	2.0.5	2.0.5	2.0.5	2.0.5	2.0.5
FreeBSD:14:latest	2.0.5	2.0.6	2.0.4	2.0.5	2.0.6	2.0.4	-	2.0.4
FreeBSD:14:quarterly	2.0.5	2.0.5	-	2.0.5	2.0.5	2.0.5	2.0.5	2.0.5
FreeBSD:15:latest	2.0.6	2.0.6	n/a	2.0.6	n/a	2.0.5	2.0.5	2.0.5

Dependencies

NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:

ruby32 : lang/ruby32
gem : devel/ruby-gems

Runtime dependencies:

ruby32 : lang/ruby32
gem : devel/ruby-gems

Patch dependencies:

ruby32 : lang/ruby32
gem : devel/ruby-gems

Extract dependencies:

ruby32 : lang/ruby32

This port is required by:

for Run

Configuration Options:

No options to configure

Options name:

biology_rubygem-bio

USES:

gem

FreshPorts was unable to extract/find any pkg message

Master Sites:

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https://rubygems.org/downloads/

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Number of commits found: 14

Commit	Credits	Log message
Commit History - (may be incomplete: for full details, see links to repositories near top of page)
2.0.6 19 Mar 2025 03:46:26	Po-Chuan Hsieh (sunpoet)	biology/rubygem-bio: Update to 2.0.6 Changes: https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc
2.0.5 30 Sep 2023 00:46:30	Po-Chuan Hsieh (sunpoet)	biology/rubygem-bio: Update to 2.0.5 Changes: https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc
2.0.4 14 Jan 2023 23:08:33	Muhammad Moinur Rahman (bofh)	Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby Switch from Mk/bsd.ruby.mk to Mk/Uses/ruby.mk Notable changes are. - Mk/bsd.ruby.mk is moved to Mk/Uses/ruby.mk. - USE_RUBY=yes is replaced with USES=ruby. - USE_RUBY_EXTCONF is replaced with USES=ruby:extconf. - USE_RUBY_RDOC is replaced with USES=ruby:rdoc. - USE_RUBY_SETUP is replaces with USES=ruby:setup. - RUBY_NO_BUILD_DEPENDS and RUBY_NO_RUN_DEPENDS are replaced with USES=ruby:{build,none,run}. - RUBY_REQUIRE isn't used anywhere, so removed. - USES=gem now implies USES=ruby. This is mainly the work of yasu@ at https://reviews.freebsd.org/D27863 I have just made some cosmetic changes and ran exp-run to test that the tree is not in a BROKEN state. Approved by: portmgr Differential Revision: https://reviews.freebsd.org/D37925
2.0.4 03 Oct 2022 02:17:49	Po-Chuan Hsieh (sunpoet)	biology/rubygem-bio: Update to 2.0.4 Changes: https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc
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)
2.0.3 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 )
2.0.3 20 Jul 2022 14:20:57	Tobias C. Berner (tcberner)	biology: remove 'Created by' lines A big Thank You to the original contributors of these ports: * Aaron Dalton <aaron@FreeBSD.org> * Akinori MUSHA aka knu <knu@idaemons.org> * Andrey Zakhvatov * Bob Zimmermann <rpz@cse.wustl.edu> * Camson Huynh <chuynh@biolateral.com.au> * Dan Siercks <dsiercks@uwm.edu> * Fernan Aguero <fernan@iib.unsam.edu.ar> * Hannes Hauswedell <h2+fbsdports@fsfe.org> * J. Bacon <jwb@FreeBSD.org> * Jason Bacon <jwb@FreeBSD.org> * Jeremy <karlj000@unbc.ca> (Only the first 15 lines of the commit message are shown above )
2.0.3 11 Jan 2022 18:47:28	Po-Chuan Hsieh (sunpoet)	biology/rubygem-bio: Update to 2.0.3 Changes: https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc
2.0.2 30 Jun 2021 20:44:06	Po-Chuan Hsieh (sunpoet)	biology/rubygem-bio: Update to 2.0.2 Changes: https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc
2.0.1 06 Apr 2021 14:31:07	Mathieu Arnold (mat)	Remove # $FreeBSD$ from Makefiles.
2.0.1 24 Jul 2020 07:49:43	sunpoet	Update to 2.0.1 Changes: https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc
1.5.2 21 Sep 2018 18:08:24	sunpoet	Update to 1.5.2 Changes: https://github.com/bioruby/bioruby/blob/bioruby-1.5/RELEASE_NOTES.rdoc
1.5.1 06 Feb 2017 23:03:17	sunpoet	Update to 1.5.1 - Update LICENSE - Add LICENSE_FILE Changes: https://github.com/bioruby/bioruby/blob/bioruby-1.5/RELEASE_NOTES.rdoc https://github.com/bioruby/bioruby/blob/master/doc/RELEASE_NOTES-1.5.0.rdoc
1.4.3.0001_1 05 Feb 2017 04:26:56	sunpoet	Move devel/rubygem-bio to biology/rubygem-bio

Number of commits found: 14

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