ena-upload-cli 0.1

Command Line Interface to upload data to the European Nucleotide Archive

ENA upload tool

About

The program submits experimental data and respective metadata to the European Nucleotide Archive (ENA). The metadata should be provided in separate tables corresponding to the following ENA objects:

• STUDY
• SAMPLE
• EXPERIMENT
• RUN

The program to perform the following actions:

• add: add an object to the archive
• modify: modify an object in the archive
• cancel: cancel a private object and its dependent objects (under development)
• release: release a private object immediately to the public (under development)

The tool dependencies in LINUX

• curl
• Genshi
• subprocess
• shlex
• json
• argparse
• hashlib
• ftplib
• uuid
• datetime
• lxml
• pandas

Installation

Linux/macOS:

sudo python3 -m pip install git+git://github.com/usegalaxy-eu/ena-upload-cli.git

Test the tool

This is still a developmental version, please run the tool in the program directory for now.

inputs:

• metadata tables
  • examples in example_table
  • Please define actions in status column e.g. add, modify, cancel, release
  • to perform bulk submission of all objects, the aliases ids in different ENA objects should be in the association where alias ids in experiment object link all objects together
• experimental data
  • examples in example_data

outputs:

• In the same directory of inputs
• metadata tables with updated info in status and other relevant columns, e.g:
  • updated status: added, modified, canceled, released
  • accession ids
  • submission date

test command: add metadata and sequence data

python ena_upload.py --action add --center 'your_center_name' --webin_id your_id --password your_password --study example_tables/ENA_template_studies.tsv --sample example_tables/ENA_template_samples.tsv --experiment example_tables/ENA_template_experiments.tsv --run example_tables/ENA_template_runs.tsv --data example_data/*gz

test command: modify a metadata

python ena_upload.py --action modify --center 'your_center_name' --webin_id your_id --password your_password --study example_tables/ENA_template_studies-2020-05-01T14\:21.tsv