Creating your EAR

We provide different options to produce the EAR:

Option A: With all the results finished, complete the YAML file and run the script to get the pdf

If you have the required results, you can complete the YAML file (take a look at EAR_basic_template.yaml and mEleMax1_example.yaml files) and run the make_EAR.py script. We recommend installing the provided conda environment to handle the program's requirements easily.

# Clone this repository to obtain all the required files
git clone https://github.com/ERGA-consortium/EARs.git

# Create the EAR environment to run the script
conda env create -f EAR_env.yml

# Filling the YAML file for your species: Using a text editor, add the values and paths of your species and the assembly process in the YAML file.
# Please use as a guide the example files EAR_basic_template.yaml and example/mEleMax1.2_EAR.yaml

# Run the script to obtain the EAR pdf
python make_EAR.py mySpecies_EAR.yaml

Option B: Run most of the analysis in Snakemake to produce a filled YAML, and run the script to get the pdf

[IN PREPARATION] Using the snakemake-based tool GEP. By means of this pipeline, you can run all the analysis in one take for pre and post-curation -pseudo-haplotype(s) (with the only exception of contamination Blobplot) and obtain the YAML file to run the make_EAR.py script with minimal manual inputs (before running the script, you would only need to edit the YAML file to enter information like name and affiliation, Blobplot PNG, contact maps link in the web, and curation notes). Remember to run with --config EAR=True, for instance (in this case using Slurm in a computer cluster):

nohup snakemake --profile SUBMIT_CONFIG/slurm/ --config EAR=True &

Option C: With all the results finished, add the required files on the Galaxy built-in tool to get the pdf

If you have all your results files in Galaxy, run the built-in tool to produce the EAR pdf.

If you are not already using Galaxy, you will need to create a Galaxy account and upload all the required results asked in the built-in tool to produce the EAR pdf.

Option D: Produce all the results on Galaxy and get the pdf

If you are not already using Galaxy, you will need to create a Galaxy account (with enough space, you can request the necessary quota for your project) and upload your final pre and post curation assemblies and WGS accurate reads for Kmer database creation to run the Galaxy ERGA Assembly Review (EAR) Analysis + Report workflow. This workflow will run genoscope, gfastats, busco and merqury. Other results (blobplot and pretext PNGs, pretext file link) must be provided.