ena-upload-cli 0.4.2

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)

After a successful submission, new tsv tables will be generated with the ENA accession numbers filled in along with a submission receipt.

Tool dependencies

• python 3.5+ including following packages:
  • Genshi
  • lxml
  • pandas
  • requests

Installation

pip install ena-upload-cli

Usage

Minimal:  ena-upoad-cli --action {add,modify,cancel,release} --center CENTER_NAME  --secret SECRET

All supported arguments:

  -h, --help            show this help message and exit
  --version             show program's version number and exit
  --action {add,modify,cancel,release}
                         add: add an object to the archive
                         modify: modify an object in the archive
                         cancel: cancel a private object and its dependent objects
                         release: release a private object immediately to public
  --study STUDY         table of STUDY object
  --sample SAMPLE       table of SAMPLE object
  --experiment EXPERIMENT
                        table of EXPERIMENT object
  --run RUN             table of RUN object
  --data [FILE [FILE ...]]
                        data for submission
  --center CENTER_NAME  specific to your Webin account
  --checklist CHECKLIST
                        specify the sample checklist with following pattern: ERC0000XX, Default: ERC000011
  --tool TOOL_NAME      specify the name of the tool this submission is done with. Default: ena-upload-cli
  --tool_version TOOL_VERSION
                        specify the version of the tool this submission is done with
  --no_data_upload      Indicate if no upload should be performed and you like to submit a RUN object (e.g. if uploaded was done separately).
  --secret SECRET       .secret.yml file containing the password and Webin ID of your ENA account
  -d, --dev             flag to use the dev/sandbox endpoint of ENA

Mandatory arguments: --action, --center and --secret.

ENA Webin

A Webin can be made here if you don't have one already. The --webin_id parameter makes use of the full username looking like: Webin-XXXXX. Visit Webin online to check on your submissions or dev Webin to check on test submissions.

The .secret.yml file

To avoid exposing your credentials through the terminal history, it is recommended to make use of a .secret.yml file, containing your password and username keywords. An example is given in the root of this directory.

ENA sample checklists

You can specify ENA sample checklist using the --checklist parameter. By default the ENA default sample checklist is used supporting the minimum information required for the sample (ERC000011). The supported checklists are listed on the ENA website. This website will also describe which Field Names you have to use in the header of your sample tsv table. The Field Names will be automatically mapped in the outputted xml if the correct --checklist parameter is given.

Fixed sample columns

The command line tool will automatically fetch the correct scientific name based on the taxon ID or fetch the taxon ID based on the scientific name. Both can be given and no overwrite will be done.

• Mandatory: alias, title, sample_description and either scientific_name or taxon_id (preferred)
• Optional: common_name

alias	title	taxon_id	scientific_name	common_name	sample_description
sample_alias_4	sample_title_2	2697049	Severe acute respiratory syndrome coronavirus 2	covid-19	sample_description_1
sample_alias_5	sample_title_3	2697049	Severe acute respiratory syndrome coronavirus 2	covid-19	sample_description_2

Viral submissions

If you want to submit viral samples you can use the ENA virus pathogen checklist by adding ERC000033 to the checklist parameter. Check out our viral example command as demonstration. Please use the ENA virus pathogen checklist on the website of ENA to know which values are allowed/possible in the restricted text and text choice fields.

Dev instance

By default the submission will be done using following url to ENA: https://www.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA

Use the --dev flag if you want to do a test submission using the tool by the sandbox dev instance of ENA: https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA. A TEST submission will be discarded within 24 hours.

Submitting a selection of rows to ENA

Optionally you can add a status column that contains the action you want to apply during this submission. If you chose to add only the first 2 samples to ENA, you specify --action add as parameter in the command and you add the add value to the status column of the rows you want to submit as demonstrated below. Same holds for the action modify.

alias	status	title	scientific_name
sample_alias_4	add	sample_title_1	homo sapiens
sample_alias_5	add	sample_title_2	human metagenome
sample_alias_6		sample_title_3	homo sapiens

The data files

Supported data

• Read data
• Genome Assembly
• Transcriptome Assembly
• Template Sequence
• Other Analyses

Most files uploaded to the ENA FTP server need to be compressed.

More information on how ENA wants to receive the files can be found here.

Note for data upload: Uploaded files are persistently stored on the ENA server after the upload for some time. Thus, if multiple test submission are performed, it is possible to skip the data upload with --no_data_upload in subsequent submissions. This also allows uploading (large) datasets separately e.g. with aspera. For the --no_data_upload argument, data file(s) still need to be provided with --data if a RUN object is submitted in order to generate MD5 sums.

Tool overview

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 the tool

• add metadata and sequence data

  ena-upload-cli --action add --center 'your_center_name' --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 --dev --secret .secret.yml
  

• modify metadata

  ena-upload-cli --action modify --center 'your_center_name' --sample example_tables/ENA_template_samples_modify.tsv --dev --secret .secret.yml
  

• viral data

  ena-upload-cli --action add --center 'your_center_name' --study example_tables/ENA_template_studies.tsv --sample example_tables/ENA_template_samples_vir.tsv --experiment example_tables/ENA_template_experiments.tsv --run example_tables/ENA_template_runs.tsv --data example_data/*gz --dev --checklist ERC000033 --secret .secret.yml
  

Note for Windows users: Windows, by default, does not support wildcard expansion in command-line arguments. Because of this the --data example_data/*gz argument should be substituted with one containing a list of the data files. For this example, use:

--data example_data/ENA_TEST1.R1.fastq.gz example_data/ENA_TEST2.R1.fastq.gz example_data/ENA_TEST2.R2.fastq.gz