BioLinux: Difference between revisions

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Latest revision as of 06:39, 27 May 2025

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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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; 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, packages can be installed via pre-compiled binary packages onare maintained for some platforms,. or buildPackages 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 ==