(Fix some links, add a possible yum command for the metapackage) |
|||
| Line 4: | Line 4: | ||
== Summary == | == Summary == | ||
Make [http://bioconductor.org | Make [http://bioconductor.org Bioconductor] available for Fedora | ||
"Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data." | "Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data." | ||
| Line 64: | Line 64: | ||
The users should be able to download the libraries and start to work with it without problem. | The users should be able to download the libraries and start to work with it without problem. | ||
In addition it might be interesting to create a package group Bioconductor, which allows to install those packages and their dependencies all at once. | In addition it might be interesting to create a package group Bioconductor, which allows to install those packages and their dependencies all at once. i.e. a "metapackage" such as R-Bioconductor: | ||
yum install R-Bioconductor | |||
== Dependencies == | == Dependencies == | ||
| Line 88: | Line 90: | ||
* http://r-project.org | * http://r-project.org | ||
* http://cran.r-project.org/mirrors.html | * http://cran.r-project.org/mirrors.html | ||
* [ | * [[Packaging/R| R packaging guidelines]] | ||
== Release Notes == | == Release Notes == | ||
Revision as of 00:54, 20 July 2008
Bioconductor
Summary
Make Bioconductor available for Fedora
"Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data."
Owner
- Name: PierreYvesChibon
Current status
- Targeted release: Fedora11
- Last updated: 19 July 2008
- Percentage of completion: 10%
Detailed Description
Bioconductor is a large R libraries repository widely used in bioinformatics for statistical analysis of genomic data.
Benefit to Fedora
Widely used packaging Bioconductor would offer a good way to promote Fedora as desktop platform for bioinformaticians.
In addition it could also be promoted in RHEL since some servers running RHEL are used to process the analysis that bioconductor offers.
Scope
Bioconductors contains around 300 packages, not all will be packaged in Fedora (at least not at first). I think for the feature the basis packages of bioconductor should be done.
Bioconductor has its own installation script in R which enable to install the basis libraries of Bioconductor.
These libraries are
- affy
- affydata
- affyPLM
- annaffy
- annotate
- Biobase
- Biostrings
- DynDoc
- gcrma
- genefilter
- geneplotter
- hgu95av2.db
- limma
- marray
- matchprobes
- multtest
- ROC
- vsn
- xtable
- affyQCReport.
The problem is that those libraries can have a high amount of dependencies.
Test Plan
Install the RPMs and test them
User Experience
The users should be able to download the libraries and start to work with it without problem.
In addition it might be interesting to create a package group Bioconductor, which allows to install those packages and their dependencies all at once. i.e. a "metapackage" such as R-Bioconductor:
yum install R-Bioconductor
Dependencies
They are included in the R libraries, most of them are in Bioconductor, some can be in the CRAN repository.
The question of the metadata and experiment data packages should be taken into account. These are heavy packages which do not evolve lot between release. Two of them are incorporated already into Fedora, they brought the question of inheritance between the version.
There is a "small" graph showing the relation (only "Requires") of the Bioconductor packages
Contingency Plan
None
Planning
- Find interested contributors
- Get a clear view on the amount of packages that have to be done
- Package and review them
Documentation
- http://bioconductor.org
- http://r-project.org
- http://cran.r-project.org/mirrors.html
- R packaging guidelines
Release Notes
None