Running bcbio.rnaseq with correct formula

Question

[L. A. Liggett]

I am using bcbio.rnaseq to analyze my bcbio analysis, but am having some trouble specifying the 'formula'. I have 9 samples 3 biological replicates of each condition. How do I input this when calling bcbio-rnaseq? This is what I'm trying:

bcbio-rnaseq summarize /dir/bcbio-project-file.yaml -o human

The only output I get is:

WARNING: update already refers to: #'clojure.core/update in namespace: incanter.core, being replaced by: #'incanter.core/update

Usage: bcbio-rnaseq summarize bcbio-project-file.yaml

Options:   -h, --help   -f, --formula FORMULA      Formula to use in model (example: ~ batch + condition)   -d, --dexseq               Run DEXSeq   -o, --organism ORGANISM    organism (mouse, human)   -s,
--sleuth               Run Sleuth

Answer 1

[L. A. Liggett]

It turns out that this was a problem with parsing a directory containing spaces in it. This will get updated in the next release.