Here you will find all the code needed to run PaleoProPhyler. PaleoProPhyler is a compliation of pipelines to enable easier and more reproducable paleoproteomic phylogenetic analyses. These pipelinese take the form of Snakemake scripts coupled with Conda enviroments and below you can find a step by step tutorial on how to run them on your local linux machine or your labs server!
Huh interesting, how do they work?
All of the scripts are based on Snakemake and Conda. I highly recomend reading through the tutorial if you want to use them. The pipelines are split up and the subcomponents are designed to function semi-independently but can also be used one after the other, as they intrinsically synergise. Each pipelinehas its own folder, which contains the Snakemake script, a YAML (.yml) file to create the conda environment, additional R and/or python scripts utilised by the pipeline as well as some example files.
The 3 pipelines are:
1) Dataset Initialization:
Easily download reference proteins/proteomes and fetch all resources required for the translation through the 'Dataset Construction' module.
2) Dataset Construction:
Translate proteins from Whole Genome datasets. Supports BAM,CRAM and VCF files as input. Data needs to be mapped onto an annotated reference genome from Ensemb
3) Dataset Analysis:
Align a proteomic dataset, format and prepare it for a phylgenetic analysis. Run phylogenetic trees including for each individual protein of the dataset and for a concatenation of all of the available proteins.
If you want to try to use PalaeoProPhyler, please see the Tutorial on how to install and use each of its pipelines.
If you want to have a detailed explanation of what is happening "under the hood" in each of the modules of PalaeoProPhyler, you can read about it in the supplementary file. This should provide you with a text explanation as well as commands and links* to scripts. Note *:The links only work if you download the pdf file, unfortunately Github's PDF viewer has some limits.
The pipelines/workflows presented here use, multiple publicly available software. All of the software and packages used by the pipelines are installed through the conda environments available here ( see Tutorial ). For the full list of the software and packages used, check out the last pages of the supplementary file:
Users with experience in conding/bioinformatics are free to alter, add or remove steps of the pipelines if they see fit. If you do that however and use the altered version of the pipeline in a publication, make sure you record and mention every alteration! I would suggest updating the conda environments with any new software that you add and uploading on Github the entire folder of the altered workflows.
It appears the current conda version of MrBayes has some issues running on some server systems. So far it's unclear what the problem is exactly, the tool will install but will not execute. So far, only servers that use Slurm have had this issue. MrBayes has thus been 'turned off' by default in the pipeline. Users can look to the RevBayes output as a Bayesian 'substitute' tool. Users who still want to try running MrBayes however, can turn it back on but removing the '#' on this file: Proteomic_Pipeline/blob/main/Dataset_Analysis/Snakefile on line 134, in their locally installed version of the pipeline.
Errors, issues and suggestions can be reported either directly to my current work email : ioannis.patramanis@sund.ku.dk , or more preferably through this github repository's issue page here.
When reporting errors, please include the following information:
a) On which module does the error occur?
b) Was the installation of the module successful?
c) Are there any output file generated?
d) Can you please provide a screenshot or a copy of the error message, if there is any.
PalaeoProPhyler is released under the MIT License