A proof of concept of a Phylogenetic pipeline intended to show Nextflow scripting and reproducibility capabilities.
To run phytoy-NF you need to install nextflow, by simply checking if you have Java 7+ and if yes, by then typing the following command:
curl -fsSL get.nextflow.io | bash
If you want to replicate exactly the pipeline and/or not install all the dependencies phytoy-NF has, then you also need to install Docker and run phytoy-NF with the '-with-docker' flag, as demonstrated below. Otherwise all the dependencies of phytoy-NF have to be installed and put in the PATH.
Install Docker on your computer. Read more here https://docs.docker.com
You can run phytoy-NF using the following commands:
-> natively:
nextflow run phytoy [phytoy-nf command line options]
-> with Docker:
nextflow run phytoy -with-docker [phytoy-nf command line options]
For example:
nextflow run phytoy -with-docker
This command will run (by automatically cloning the respository in your workstation, due to the Nextflow integration with github) the analysis for the "hip.fa" and "seatoxin.fa" example-datasets contained in the data/ directory, and will generate a multiple sequence alignmnet and a phylogenetic tree for each dataset.
--in_dir Directory containing one or more protein sequence datasets in fasta format to be analysed
--out_dir Output directory
phytoy-NF uses the following external programs (which have to exist in the PATH if the pipeline is executed without docker):
t-coffee http://www.tcoffee.org/Packages/Stable/Version_11.00.8cbe486/linux/T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.tar.gz
raxml https://github.com/stamatak/standard-RAxML/archive/v8.0.0.zip