Data submission to ENA - Intro

We will submit our analysis to ENA now. We will use the ENA dev/test Server for all submissions. Submissions sent there will be deleted every night, so it is a good environment for all kind of tests regarding submissions.

Structure of this lesson

The aim of this lesson is to submit everything we generated so far: raw data, assembly, binning and MAGs. To reduce the amount of work, we will submit one bin/MAG after the submission of assemblies. The complete submission will work in the following order:

  1. Create a study

  2. Create a sample

  3. Submit raw reads

  4. Submit the assembly results

  5. Create a sample for the selected bin we want to submit

  6. Submit the bin

  7. Create a sample for the selected MAG we want to submit

  8. Submit the MAG (do the annotation with prokka before doing that)

So there is a lot to be done. Let’s get started by getting webin-cli - a command line tool provided by ENA to allow/facilitate some submissions on the command line

Getting webin-cli

Getting webin-cli is easy - just get the latest jar from this git repository:

https://github.com/enasequence/webin-cli/

As of today, the latest version is 6.10.0, get it using wget:

cd
https://github.com/enasequence/webin-cli/releases/download/6.10.0/webin-cli-6.10.0.jar

If you want, you can read the help message with:

java -jar ~webin-cli-6.10.0.jar -help

We will need that tool in later steps. Study and sample will be created in the web interface and bin samples will be submitted using curl.

Set credentials as environment variables

To not type your username password every time you submit, you should store them as environment variables:

export ENA_USER=Webin-xxxx
export ENA_PWD=password

This will allow you, to just copy and paste the submit commands in this documentation.