A series of pipelines for running tools (currently MetaPhlAn2 and HUMAnN2) from the bioBakery collection developed by the Huttenhower lab within the CGAT framework.
Requires installation of MetaSequencing and CGATCore. The latter is a framework for running bioinformatics pipelines built around the Ruffus library that automatically handles job submission on HPC clusters. CGAT installation instructions can be found here.
It also requires installtion of the various BioBakery tools, which should be available in the PATH. Additionally these tools can be installed to a virtual envrionment that will be initiated before references to their commands.
Pipelines are run from the working directory containing the files to be analysed. First a config file pipeline.yml must be generate in the directory using the config command. The pipeline can then be run using make full
An example run for Humann2 is shown below:
#make an analysis folder and symlink the starting reads
mkdir Humann2_Run
cd Humann2_Run
ln -s path_to_reads/*.gz ./
#generate the pipeline configuration file (this will need to be edited to set parameters)
python CGATBioBakery/pipelines/pipeline_humann2.py config
#run the full humann2 run (this will also merge and normalise the output tables)
python CGATBioBakery/pipelines/pipeline_humann2.py make full