Arthur Zwaenepoel (2018-2019)
Nextflow pipeline and other utilities for preparing an analysis with Whale. The pipeline does:
- Alignment with PRANK
- MCMC with MrBayes
- CCD construction aith ALEobserve
The dependencies are nextflow, python3, PRANK, MrBayes and ALEobserve. The pipeline is configured to work with SGE cluster environments, and should be submitted from the head node.
If you haven't installed the nextflow or not familiar with nextflow, we recommend a brief tutorial on nextflow. To install the nextflow, try the following command
curl -s https://get.nextflow.io | bash
To run the pipeline in a virtualenv environment, do
virtualenv -p=python3 ENV_whaleprep
source $PATH/ENV_whaleprep/bin/activate
$PATH/nextflow whaleprep.nf --fasta <fastadir> --tools $PATH/whaleprep.py
where fastadir is directory with multifasta files of protein sequences for all
gene families of interest (one file per family). Optional arguments currently are:
--tools path to whaleprep.py
--out output directory name
--ngen number of MCMC generations used in MrBayes
--samplefreq sample frequency for the MCMC
--burnin the number of samples to discard as burn-in in ALEobserve
Please make sure that there is no "-" in the gene name, otherwise the mrbayes might have error.
Notes on updates: the Bio.Alphabet module is removed from Biopython 1.78 (September 2020),see the document, the biopython<=1.77 is now required, please try
pip install biopython==1.77