eva-sub-cli

EVA Submission Command Line Interface for Validation

Installation

There are currently three ways to install and run the tool: using conda, from source using Docker, and from source natively (i.e. managing dependencies on your own).

Conda

The most straightforward way to install eva-sub-cli and its dependencies is through conda. For example the following installs eva-sub-cli in a new environment called eva, activates the environment, and prints the help message:

conda create -n eva -c conda-forge -c bioconda eva-sub-cli
conda activate eva
eva-sub-cli.py --help

From source using Docker

Docker provides an easy way to run eva-sub-cli without installing dependencies separately. This method requires just Python 3.8+ and Docker to be installed. Then either clone the git repository, or download the newest tagged release from here:

git clone [email protected]:EBIvariation/eva-sub-cli.git
# OR (replace "v0.2" with the newest version)
wget -O eva-sub-cli.zip https://github.com/EBIvariation/eva-sub-cli/archive/refs/tags/v0.2.zip
unzip eva-sub-cli.zip && mv eva-sub-cli-* eva-sub-cli

Then install the library and its dependencies as follows (e.g. in a virtual environment):

cd eva-sub-cli
# Activate your virtual environment 
python -m pip install .

To check it is installed correctly, you can run:

eva-sub-cli.py -h

From source natively

This method requires the following:

• Python 3.8+
• Nextflow 21.10+
• biovalidator 2.1.0+
• vcf-validator 0.9.6+

Install each of these and ensure they are available on the path. Then git clone the repo or install the newest release as described above.

Input files for the validation and submission tool

There are two ways of specifying the VCF files and associated reference genome

Using --vcf_files and --reference_fasta

This allows you to provide multiple VCF files to validate and a single associated reference genome file. The VCF files and the associated reference genome file must use the same chromosome naming convention

Using metadata file by providing --metadata_json or --metadata_xlsx

The path to the VCF files are provided in the Files section of the metadata and their corresponding fasta sequence is provided in the analysis section. This allows us to support different assemblies for each VCF file. Please check the below sections The metadata spreadsheet and The metadata JSON for the format and options available in metadata files.

The metadata spreadsheet

The metadata template can be found within the etc folder at eva_sub_cli/etc/EVA_Submission_template.xlsx It should be populated following the instruction provided within the template

The metadata JSON

The metadata can also be provided via a JSON file which should conform to the schema located at eva_sub_cli/etc/eva_schema.json

More detail documentation to follow

Execution

Note for Docker users: for each of the below commands, add the command line option --executor docker, which will fetch and manage the docker container for you. Make sure that Docker is running in the background, e.g. by opening Docker Desktop.

Validate and submit your dataset

To validate and submit run the following command

eva-sub-cli.py --metadata_xlsx metadata_spreadsheet.xlsx \
               --vcf_files vcf_file1.vcf vcf_file2.vcf --reference_fasta assembly.fa --submission_dir submission_dir

Validate only

To validate and not submit run the following command

eva-sub-cli.py --metadata_xlsx metadata_spreadsheet.xlsx --submission_dir submission_dir --tasks VALIDATE

Submit only

All submission must have been validated. You cannot run the submission without validation. Once validated running

eva-sub-cli.py --metadata_xlsx metadata_spreadsheet.xlsx --submission_dir submission_dir

or

eva-sub-cli.py --metadata_xlsx metadata_spreadsheet.xlsx --submission_dir submission_dir --tasks SUBMIT

Will only submit the data and not validate.