Principals, Practices, and Habits
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Some ideas I presented to a bioinformatics core about software development, literate programming, and versioning.
Principals, Practices, and Habits
- 1. Principles, Practices, and HabitsJeremy LeipzigDecember 18, 2010
- 2. Gearing up for a data delugeTechnicalScientificCulturalVersion controlDocumentationTestingLiterate programming
- 3. Principles, Practices, and Habits
- 4. Results belong in reports, not emailsAnswer a question onceConstant improvementAssociate results with a set of stated parameters
- 5. Literate programmingDynamic reportsReproducible outputMarry code to reportsMarry data & configuration to reportsReinforced sanity
- 6. SweaveR +In R:Sweave(¡°myReport.Rnw¡±,output=¡±myReport.tex¡±)In shell:echo "Sweave(\"myReport.Rnw\",output=\"myReport.tex\");" | R --no-save --quietIn shell:pdflatexmyReport.texchromosomeBias.Rnw sample:svn co http://versioncontrol.chop.edu/svn/cbmi/chipSeq/trunk/chipSeqScriptsecho "configFile<-\"bias.config.R\";Sweave(\¡±chromosomeBias.Rnw\",output=\"chromosomeBias.tex\");" | R --no-save --quiet
- 8. VersioningSubversion keyword substitutionsvn add chromosomeBias.Rnwsvnpropsetsvn:keywords 'Revision' chromosomeBias.Rnwsvnci ¨Cm ¡°added chromosomeBiassweave script¡±$Rev$http://svnbook.red-bean.com/en/1.5/svn.advanced.props.special.keywords.html
Editor's Notes
- #4: Parameterize90% time futzing with figure graphics, legendsCloud computing design architectures