scipion-em-empiar 3.0.6

A Scipion plugin to make depositions to EMPIAR

Scipion Empiar Depositor

This project is a Scipion plugin to make depositions to https://www.ebi.ac.uk/pdbe/emdb/empiar

Setup

In order to install the plugin follow these instructions:

1. Install this plugin:

scipion installp -p scipion-em-empiar

or through the plugin manager by launching Scipion and following Configuration >> Plugins

Alternatively, in devel mode:

git clone https://github.com/scipion-em/scipion-em-empiar.git
scipion installp -p local/path/to/scipion-em-empiar --devel

2. Download Aspera Connect:

Go to https://www.ibm.com/aspera/connect/ and download the latest version.

3. Register an account in the EMPIAR deposition and Segmentation Annotation Tool

Go to https://www.ebi.ac.uk/pdbe/emdb/empiar/deposition/register/ and get an API token at Get empiar-deposition API token section

4. Open scipion’s config file ‘scipion3 config –show’ and add the following variables:

ASCP = <aspera_binary_path> (usually it is located at $HOME/.aspera/connect/bin/ascp)
ASPERA_SCP_PASS= <aspera_shares_user_password>
EMPIAR_TOKEN = <empiar_token>

NOTE: If you want to create a Workflow RO-Crate (https://about.workflowhub.eu/Workflow-RO-Crate/) you must have Graphviz installed (https://graphviz.org/download/)