Shaun Jackman @sjackman
2014-10-09 at VanBUG, Vancouver, Canada
Given the same data and code…
Given the manuscript…
Another scientist can
Reproducibility is fundamental to science
We used Linuxbrew to install the required software from Homebrew-science version 2014-08.
Best way to set back your competitors is to release your #data. That way they have to analyze their data & your data
Tell Make how to create one type of file from another
and which files you want to create.
Make looks at which files you have
and figures out how to create the files that you want.
%.bam: %.sam samtools view -Sb $< >$@ %.sort.bam: %.bam samtools sort $< $*.sort %.bam.bai: %.bam samtools index $<
touch hello.sam make hello.sort.bam.bai
samtools view -Sb hello.sam >hello.bam samtools sort hello.bam hello.sort samtools index hello.sort.bam
Markdown is a plain-text typesetting language
A header ======== A list: + This text is *italic* + This text is **bold**
Pandoc renders attractive documents and slides
from plain-text typesetting formats
It converts between every format known (just about)