Latest revision as of 13:25, 7 November 2015

Bioconductor

NOTE: the information in this article is very outdated (targets Fedora 12).

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: Fedora 12
Last updated: 21 March 2009
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

Bioconductor name	Fedora package	Review request
affy		515081
affydata		591447
affyPLM
~~annaffy~~		depends on KEGG.db which is non-free
annotate
Biobase	R-Biobase	#240500
Biostrings	R-Biostrings	#490721
DynDoc	R-DynDoc	#241079
gcrma
genefilter
geneplotter
hgu95av2.db
limma
marray
matchprobes
multtest	R-multtest	240497
ROC		591737
vsn
xtable		591032
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 "Depends") of the Bioconductor packages

There is a list showing for each packages from the base list their dependencies and their sub-dependencies:

Contingency Plan

None -- What should that be ??

Planning

Find interested contributors
Get a clear view on the amount of packages that have to be done
Package and review them

Documentation

---

R2spec - Small script to easily create the specfile of R libraries
updateCVS.py - Small script to easily update R library on Fedora CVS
bio.pl and showDep.py to retrieve the list of dependencies of the Bioconductor libraries and parse them for the libraries of interest.

Release Notes

None -- What should that be ?

@@ Line 1: / Line 1: @@
 = Bioconductor =
+'''NOTE: the information in this article is very outdated (targets Fedora 12).'''
 == Summary ==
-Make [http://bioconductor.org |Bioconductor] available for Fedora
+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."
 == Owner ==
-* Name: PierreYvesChibon
+* Name: [[User:Pingou|PierreYvesChibon]]
 == Current status ==
-* Targeted release: [[Releases/11|  Fedora11]]
+* Targeted release: [[Releases/12|  Fedora 12]]
-* Last updated: 19 July 2008
+* Last updated: 21 March 2009
 * Percentage of completion: 10%
@@ Line 33: / Line 34: @@
 These libraries are
-# affy
-# affydata
+{|
-# affyPLM
+|Bioconductor name||Fedora package||Review request
-# annaffy
+|-
-# annotate
+| [http://www.bioconductor.org/packages/bioc/html/affy.html affy] || || [https://bugzilla.redhat.com/show_bug.cgi?id=515081 515081]
-# Biobase
+|-
-# Biostrings
+| [http://www.bioconductor.org/packages/release/data/experiment/html/affydata.html affydata] || || [https://bugzilla.redhat.com/show_bug.cgi?id=591447 591447]
-# DynDoc
+|-
-# gcrma
+| [http://www.bioconductor.org/packages/bioc/html/affyPLM.html affyPLM] || ||
-# genefilter
+|-
-# geneplotter
+| <strike>[http://www.bioconductor.org/packages/bioc/html/annaffy.html annaffy]</strike> || || depends on KEGG.db which is non-free
-# hgu95av2.db
+|-
-# limma
+| [http://www.bioconductor.org/packages/bioc/html/annotate.html annotate] ||  ||
-# marray
+|-
-# matchprobes
+| [http://www.bioconductor.org/packages/bioc/html/Biobase.html Biobase] || [http://admin.fedoraproject.org/pkgdb/packages/name/R-Biobase R-Biobase] || [https://bugzilla.redhat.com/show_bug.cgi?id=240500 #240500]
-# multtest
+|-
-# ROC
+| [http://www.bioconductor.org/packages/bioc/html/Biostrings.html Biostrings] || [http://admin.fedoraproject.org/pkgdb/packages/name/R-Biostrings R-Biostrings] || [https://bugzilla.redhat.com/show_bug.cgi?id=490721 #490721]
-# vsn
+|-
-# xtable
+| [http://www.bioconductor.org/packages/bioc/html/DynDoc.html DynDoc] || [http://admin.fedoraproject.org/pkgdb/packages/name/R-DynDoc R-DynDoc] || [https://bugzilla.redhat.com/show_bug.cgi?id=241079 #241079]
-# affyQCReport.
+|-
+| [http://www.bioconductor.org/packages/bioc/html/gcrma.html gcrma] || ||
+|-
+| [http://www.bioconductor.org/packages/bioc/html/genefilter.html genefilter] || ||
+|-
+| [http://www.bioconductor.org/packages/bioc/html/geneplotter.html geneplotter] || ||
+|-
+| [http://bioconductor.org/packages/release/data/annotation/html/hgu95av2.db.html hgu95av2.db] || ||
+|-
+| [http://www.bioconductor.org/packages/bioc/html/limma.html limma] || ||
+|-
+| [http://www.bioconductor.org/packages/bioc/html/marray.html marray] || ||
+|-
+| [http://www.bioconductor.org/packages/bioc/html/matchprobes.html matchprobes] || ||
+|-
+| [http://www.bioconductor.org/packages/bioc/html/multtest.html multtest] || [http://admin.fedoraproject.org/pkgdb/packages/name/R-multtest R-multtest] || [https://bugzilla.redhat.com/show_bug.cgi?id=240497 240497]
+|-
+| [http://www.bioconductor.org/packages/bioc/html/ROC.html ROC] || || [https://bugzilla.redhat.com/show_bug.cgi?id=591737 591737]
+|-
+| [http://www.bioconductor.org/packages/bioc/html/vsn.html vsn] || ||
+|-
+| [http://cran.r-project.org/web/packages/xtable/index.html xtable] || || [https://bugzilla.redhat.com/show_bug.cgi?id=591032 591032]
+|-
+| [http://www.bioconductor.org/packages/bioc/html/affyQCReport.html affyQCReport] || ||
+|}
 The problem is that those libraries can have a high amount of dependencies.
@@ Line 64: / Line 89: @@
 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 ==
@@ Line 72: / Line 99: @@
 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
+There is a "small" graph showing the relation (only "Depends") of the Bioconductor packages
-* [http://pingou.fedorapeople.org/biocpackages.svg Dependencies -SVG]
+* [http://pingou.fedorapeople.org/Bioconductor/biocpackages.svg Dependencies -SVG]
-* [http://pingou.fedorapeople.org/biocpackages2.png Dependencies -PNG]
+* [http://pingou.fedorapeople.org/Bioconductor/biocpackages2.png Dependencies -PNG]
+There is a list showing for each packages from the base list their dependencies and their sub-dependencies:
+* [http://pingou.fedorapeople.org/Bioconductor/Depedencies-Depends.txt List of dependencies for only the "Depends" libraries]
+* [http://pingou.fedorapeople.org/Bioconductor/Dependencies-Depends_Suggests.txt List of dependencies for the "Depends" and "Suggests" libraries]
 == Contingency Plan ==
-None
+None -- What should that be ??
 == Planning ==
@@ Line 88: / Line 119: @@
 * http://r-project.org
 * http://cran.r-project.org/mirrors.html
-* [packaging/R| R packaging guidelines]
+* [[Packaging/R| R packaging guidelines]]
+---
+* [https://fedorahosted.org/r2spec/ R2spec] - Small script to easily create the specfile of R libraries
+* [http://pingou.fedorapeople.org/Scripts/updateCVS_1.2.py updateCVS.py] - Small script to easily update R library on Fedora CVS
+* [http://pingou.fedorapeople.org/Scripts/bio.pl bio.pl] and [http://pingou.fedorapeople.org/Scripts/showDep.py showDep.py] to retrieve the list of dependencies of the Bioconductor libraries and parse them for the libraries of interest.
 == Release Notes ==
-None
+None -- What should that be ?
+----
-[[Category:ProposedFeature]]
+[[Category:FeaturePageIncomplete]]

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