A Scipion plugin to make depositions to EMPIAR
Project description
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:
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
Download Aspera Connect:
Go to https://www.ibm.com/aspera/connect/ and download the latest version.
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
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>
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