From Fedora Project Wiki
(→Bioinformatics packages: pypop now in repo) |
(→Bioinformatics packages: split into "in repo" and "to-be-packaged") |
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== Bioinformatics packages == | == Bioinformatics packages == | ||
===In repository=== | |||
* [http://www.bioperl.org/ bioperl] ([https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=234573 review request] ), bioperl-run ([https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=236877 review request] ) [in repo] and dependencies: | * [http://www.bioperl.org/ bioperl] ([https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=234573 review request] ), bioperl-run ([https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=236877 review request] ) [in repo] and dependencies: | ||
*(Note that the below were based upon packages originally submitted by HunterMatthews that were reviewed and approved but never built) | *(Note that the below were based upon packages originally submitted by HunterMatthews that were reviewed and approved but never built) | ||
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* [http://www.ebi.ac.uk/Wise2/ wise2] ([https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=236158 review request] ) [in repo] | * [http://www.ebi.ac.uk/Wise2/ wise2] ([https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=236158 review request] ) [in repo] | ||
* [http://www.pypop.org PyPop] - Python for Population Genomics (I am the primary upstream developer) ([https://bugzilla.redhat.com/show_bug.cgi?id=464460 review request]) [in repo] | * [http://www.pypop.org PyPop] - Python for Population Genomics (I am the primary upstream developer) ([https://bugzilla.redhat.com/show_bug.cgi?id=464460 review request]) [in repo] | ||
===To be packaged=== | |||
* [http://www.swarm.org Swarm] - agent-based modelling toolkit | * [http://www.swarm.org Swarm] - agent-based modelling toolkit | ||
Revision as of 03:58, 1 December 2008
Alex Lancaster
Mainly interested in packaging bioinformatics tools for Fedora. Member of SIGs/SciTech .
- specs and SRPMs for packages-in-review on alexlan.fedorapeople.org
- Fedora Account System: alexlan
Useful links
- My Watchlist
- PackageMaintainers/CommonRpmlintIssues , Packaging/Python , Packaging/Perl, PackagingDrafts/Perl , PackageMaintainers/NewPackageProcess , Infrastructure/UpdatesSystem/Bodhi-info-DRAFT
- Track my upstream CPAN packages: http://fedora.biggerontheinside.net/perl/alexlan.html
Bioinformatics packages
In repository
- bioperl (review request ), bioperl-run (review request ) [in repo] and dependencies:
- (Note that the below were based upon packages originally submitted by HunterMatthews that were reviewed and approved but never built)
- perl-SVG (review request ) [in repo]
- perl-GD-SVG (review request ) [in repo]
- perl-XML-Writer (review request ) [in repo]
- perl-Text-Shellwords (review request ) [in repo]
- perl-Graph (review request ) [in repo]
- (These are newly packaged by me:)
- perl-Math-Derivative (review request ) [in repo]
- perl-Math-Spline (review request ) [in repo]
- perl-Convert-Binary-C (review request ) [in repo]
- perl-XML-XPathEngine (review request ) [in repo]
- perl-XML-DOM-XPath (review request ) [in repo]
- perl-SVG-Graph (review request ) [in repo]
- perl-Post
Script (review request ) [in repo] - perl-Data-Stag (review request ) [in repo]
- perl-Ace
Perl (review request ) [in repo] - perl-Bio-ASN1-Entrez
Gene (review request ) [in repo] - perl-AutoClass (review request ) [in repo]
- (Note other deps originally by Hunter: perl-Heap, perl-MIME-Lite, perl-SOAP-Lite were not orphaned, but picked up by other maintainers)
- biopython (review request ) [in repo]
- wise2 (review request ) [in repo]
- PyPop - Python for Population Genomics (I am the primary upstream developer) (review request) [in repo]
To be packaged
- Swarm - agent-based modelling toolkit
Other packages
- picard (MusicBrainz tagger) (review request ) [in repo]
- libdiscid - dependency for libmusicbrainz/python-musicbrainz2 and also used for picard (review request ) [in repo]
- ESS : Emacs Speaks Statistics (emacs-ess) Emacs add-on package to interface with the statistical packages R, amongst others. (review request ) [in repo]
- bibus bibliography manager for Open
Office.org (review request ) [in repo] - latex2emf (review request ), small package to generate an EMF file from LaTeX source, prerequisite for OOoLaTeX extension (see below) [in repo]
- OOoLatex (review request ) Extension for OpenOffice.org to permit the entering and rendering of LaTeX equations directly in Draw/Impress documents. Depends on libEMF. [in repo]
Ready for review
Other packages I'm interested in maintaining, or helping to maintain
- SAGE: the open-source computer algebra/mathematics framework (this is a huge package with many dependencies and will require work from multiple maintainers).
- Bioconductor: bioinformatics packages for R. Many of these packages are now included in Fedora, Pingou is trying to make this a Feature.
- E-Cell: GPL-licensed cell simulator for systems biology