philarevalo/ribotree

Pipeline to make a phylogeny from ribosomal proteins pulled from microbial genomes

RiboTree

This pipeline takes as input a directory of genomes in complete or draft format (one file = one genome) and outputs a phylogeny of those genomes based on single copy ribosomal proteins. Ribosomal proteins are identified using hmmsearch and an alignment of ribosomal proteins from Yutin et al., 2012, aligned using mafft, and used to build a phylogeny with raxml. The basis for this pipeline is the method detailed in Hehemann, et al., 2016. It utilizes snakemake for ease of use and reproducibility.

##How to run

Dependencies of this pipeline are handled by conda. You can download miniconda (for python 3.5 or higher please!) here.

After installing miniconda:

1. Modify the RiboTree_config.yml file to reflect appropriate filepaths, parameters, and filenames. All parameters are described in comments within the RiboTree_config.yml file.

1b. If running on a cluster that uses slurm as a job scheduler, modify the RiboTree_cluster_params.yml file to match your cluster setup.

2a. If running on a single machine, simply run the RiboTree_run_on_single_machine.sh shell script.

2b. If running on a cluster that uses slurm as a job scheduler, modify the RiboTree_run_on_slurm.sbatch jobscript as appropriate and submit to the job scheduler.

##Notes

Not tested on Windows or OSX machines. I suspect that at present the code will break in windows due to the use of \ as opposed to / in filepaths on Windows systems. May work in OSX.

ribotree's Issues

python 3.5 is end of life

Hi,

according to the python release page python 3.5 is no more supported. Would it be possible to bump the python version to a maintained version (>=3.7) in the env.yaml? Do you think this will influence the results?

Thanks

Names for expected targets for BuildPhylo not quite correct

Pipeline finishes as expected, but snakemake can't find final files because of some issues with expected filename targets.

yaml file doesn't work

I had to remove multiple dependency versions from RiboTree_Environment.yml:

name: RiboTree
channels:
- biocore
- bioconda
dependencies:
- dropbox=5.2.1
- filechunkio=1.6
- ftputil=3.2
- pysftp=0.2.8
- snakemake=3.7.1
- urllib3=1.12
- hmmer=3.1b2
- mafft=7.245
- biopython
- docutils=0.12
- ecdsa=0.13
- libgcc=5.2.0
- mkl
- numpy=1.11.1
- openssl=1.0.2h
- paramiko
- pip
- pycrypto=2.6.1
- python=3.5.2
- pyyaml=3.11
- raxml=8.2.9
- readline=6.2
- requests=2.10.0
- setuptools=23.0.0
- six=1.10.0
- sqlite=3.13.0
- tk
- wheel=0.29.0
- xz=5.2.2
- yaml=0.1.6
- zlib=1.2.8
- pip:
  - dropbox==5.2.1
  - filechunkio==1.6
  - ftputil==3.2
  - pysftp==0.2.8
  - snakemake==3.7.1
  - urllib3==1.12