Command Line Interface to upload data to the European Nucleotide Archive
Project description
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)
Tool dependencies
- curl
- python 2.7+ including following packages:
- Genshi
- lxml
- pandas
Installation
pip install ena-upload-cli
Be aware that Windows can give problems with the
curl
commands executed by the script. Check that curl is available in your PATH.
Usage
usage: ENA_upload [-h] --action {add,modify,cancel,release} [--study STUDY]
[--sample SAMPLE] [--experiment EXPERIMENT] [--run RUN]
[--data [FILE [FILE ...]]] --center CENTER_NAME --webin_id
WEBIN_ID (--password PASSWORD | --secret SECRET) [-d]
optional arguments:
-h, --help show this help message and exit
--action {add,modify,cancel,release}
add: add an object to the archive
modify: modify an object in the
--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
--webin_id WEBIN_ID the usermane of your Webin account
--password PASSWORD the password of your Webin account
--secret SECRET .secret file containing the password of your Webin account
-d, --dev Flag to use the dev/sandbox endpoint of ENA.
--vir Flag to use the viral sample template.
Mandatory arguments: --action, --center, --webin_id, --password or --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 password parameter
To avoid exposing you password through the terminal history, it is recommended to make use of a .secret
file, containing your password on the first line. Use instead of the --password parameter in the ena-upload-cli tool the --secret parameter to specify the location of the .secret file.
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.
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.
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
- examples in
- experimental data
- examples in
example_data
- examples in
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
- updated status:
test command: add metadata and sequence data
ena_upload --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 --dev
test command: modify a metadata
ena_upload --action modify --center 'your_center_name' --webin_id your_id --password your_password --study example_tables/ENA_template_studies-2020-05-01T1421.tsv --dev
test command .secret file
ena-upload-cli --action add --center 'your_center_name' --webin_id your_id --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
test command for viral data
ena_upload --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_vir.tsv --experiment example_tables/ENA_template_experiments.tsv --run example_tables/ENA_template_runs.tsv --data example_data/*gz --dev --vir
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