EVA-3663_cli_Documentation #59
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| 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. | ||
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| ### The metadata spreadsheet | ||
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Edit for the following lines:
The metadata template can be found within the [etc folder](eva_sub_cli/etc/EVA_Submission_template.xlsx). It should be populated following the instruction provided within the template.
| ### Submit only | ||
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| All submission must have been validated. You cannot run the submission without validation. Once validated running | ||
| All submission must have been validated. You cannot run the submission without validation. Once validated, execute the following command | ||
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| ```shell | ||
| eva-sub-cli.py --metadata_xlsx metadata_spreadsheet.xlsx --submission_dir submission_dir |
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This will only submit the data and not validate.
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| ## Installation | ||
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| 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). | ||
| There are currently three ways to install and run the tool : |
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Apparently there's some cultural differences in spacing for colons... I don't mind either way, as long as we're consistent.
| ### Using metadata file by providing `--metadata_json` or `--metadata_xlsx` | ||
| | OPTIONS/PARAMETERS | DESCRIPTION | | ||
| |----------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | ||
| | --version | Shows version number of the program and exit | |
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Technically I've edited the --help text in the code... we can transfer those edits here but it's not a big deal.
Co-authored-by: April Shen <ashen@ebi.ac.uk>
tcezard
approved these changes
Sep 17, 2024
nitin-ebi
approved these changes
Sep 17, 2024
Co-authored-by: Timothee Cezard <tcezard@ebi.ac.uk>
apriltuesday
approved these changes
Sep 17, 2024
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