BioLinux: Difference between revisions

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Latest revision as of 06:39, 27 May 2025

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{{Short description|Projects involved in bioinformatics software on Linux}}

{{multiple issues|

{{original research|date=October 2009}}

{{external links|date=November 2012}}

{{third-party|date=September 2013}}

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=== BioArchLinux ===

[https://github.com/BioArchLinux/Packages BioArchLinux repository] contain more than 3,770 packages for Arch Linux and Arch Linux based distribution. <ref name="Zhang 2025">{{Cite journal|last1=Zhang|first1=Guoyi|last2=Ristola|first2=Pekka|last3=Su|first3=Han|last4=Kumar|first4=Bipin|last5=Zhang|first5=Boyu|last6=Hu|first6=Yujin|last7=Elliot|first7=Michael G|last8=Drobot|first8=Viktor|last9=Zhu|first9=Jie|last10=Staal|first10=Jens|last11=Larralde|first11=Martin|last12=Wang|first12=Shun|last13=Yi|first13=Yun|last14=Yu|first14=Haoran|date=2025|title=BioArchLinux: community-driven fresh reproducible software repository for life sciences|journal=Bioinformatics|pages=btaf106|doi=10.1093/bioinformatics/btaf106|issn=1367-4811|doi-access=free|pmc=11925497}}</ref>

[https://github.com/BioArchLinux/Packages BioArchLinux repository] contain more than 3,770 packages for Arch Linux and Arch Linux based distribution.

=== Debian ===

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; FreeBSD

[[FreeBSD]] is not a Linux distribution, but as it is a version of [[BSD|Unix]] that it is very similar. Its [[ports collection|ports]] are likeanalogous Gentoo's ebuilds, and the same caveats apply. However, therethe areproject alsocontinuously builds pre-compliedcompiled binary packages available.for ThereTier-1 areplatforms oversuch 60as biological[[x86]] sciencesand applications,[[ARM_architecture_family|ARM]]. Users can also choose to build and they'reinstall listedany onport thefrom Freshsource Ports<ref>[http://wwwin order to enable non-portable optimizations or other build options.freshports.org/biology/ Fresh Ports]</ref>The build-from-source option also allows the ports system to automate installation of software with a license that does not permit siteredistribution.

The ports collection contains over 31,000 ports, of which over 2,200 are in scientific categories, and over 240 are biology-related. New ports and updates are listed on the Fresh Ports<ref>[http://www.freshports.org/biology/ Fresh Ports]</ref> site.

; pkgsrc

The [[pkgsrc]] package manager, originally forked from [[FreeBSD ports]], is maintained by the [[NetBSD]] project, but aims to support all [[POSIX]]-compatible operating systems. It is well-tested on [[NetBSD]], many [[Linux]] distributions, [[macOS]], and [[SunOS]] derivatives. Like FreeBSD ports, pre-compiled binary packages are maintained for some platforms. Packages can be built from source on any platform, or if additional optimizations or options are desired. The pkgsrc collection contains over 19,000 packages, of which nearly 800 are in scientific categories, and over 60 are biology-related.

; Debian

There are more than a hundred bioinformatics packages provided as part of the standard Debian installation. NEBC Bio-Linux<ref>[{{Cite web |url=http://envgen.nox.ac.uk/biolinux.html |title=NEBC Bio-Linux] |access-date=2005-12-19 |archive-date=2006-04-22 |archive-url=https://web.archive.org/web/20060422152024/http://envgen.nox.ac.uk/biolinux.html |url-status=dead }}</ref> packages can also be installed on a standard Debian system as long as the bio-linux-base package is also installed. This creates a /usr/local/bioinf directory where our other packages install their software. Debian packages may also work on [[Ubuntu Linux]] or other Debian-derived installations.

== Community building and support systems ==

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== See also ==

* [[List of open-source bioinformatics software]]

* [[List of biomedical cybernetics software]]

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{{Reflist|colwidth=30em}}

==External links==

{{Free healthcare software}}