This repository contains script, tools, information about the methods/routes used to submit sample/experiment/run to European Nucleotide Archive (ENA).
Can be done by connecting on the Webin submission service
Test can be also done on their Test Webin submission service
Different xml files must be created and then submitted using a curl command.
More information about the xml files (format, etc.) can be found in the ENA readthedocs
Curl command for a test submission:
curl -u Webin-USER:PASS -F "SUBMISSION=@submission.xml" -F "SAMPLE=@sample.xml" -F "RUN=@run.xml" -F "EXPERIMENT=@exp.xml" "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/" >> runExpLog.txt 2>&1 Command to upload to ftp server:
ftp webin2.ebi.ac.ukrunExpLog.txt file stores the progress and error logs
When tests are successful, replace the url https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/ with https://www.ebi.ac.uk/ena/submit/drop-box/submit/ for publishing.
Several parser are available in the script directory for the creation of those xml files.
Only reads can be submitted using this route, samples or studies must be submitted first using one of the above method.