This is a basic differential expression analysis pipeline based developed at the Life Sciences Computation Centre, University of Melbourne.

It is based around the Tuxedo protocol (Tophat, Cufflinks) and EdgeR/Voom with HTSeq-count.

To run the pipeline you will need the Ruffus library: http://www.ruffus.org.uk/.

Documentation for the pipeline can be found here.

Usage:

python RNA-seq_pipeline.py
    [-h | --help]
    --opts=<pipeline options files>
    --style=<run | print | flowchart>
    --force=<force this task to run>
    --end=<final task>
    --rebuild=<fromtarget | fromstart>
    --verbose=<0 | 1 | 2>

Example:

python RNA-seq_pipeline.py \
    --opts=pipeline_config,pipeline_stages_config \
    --style=run \
    --end=fastQC

If arguments are not specified, the default setting listed in pipeline_config.py will be used.

Use Python 2.7.5, which you can load with

module load python-gcc/2.7.5

To use the flowchart option you will need graphviz which you can load with

module load graphviz

If you're using a terminal multiplexer (such as GNU Screen) on merri, some environment variables aren't inherited so you'll have to reload your modules.

module purge
module load vlsci/2014-09