========================
Scipion Empiar Depositor
========================
This project is a Scipion plugin to make depositions to https://www.ebi.ac.uk/pdbe/emdb/empiar or to download raw data.
.. image:: https://img.shields.io/pypi/v/scipion-em-empiar.svg
:target: https://pypi.python.org/pypi/scipion-em-empiar
:alt: PyPI release
.. image:: https://img.shields.io/pypi/l/scipion-em-empiar.svg
:target: https://pypi.python.org/pypi/scipion-em-empiar
:alt: License
.. image:: https://img.shields.io/pypi/pyversions/scipion-em-empiar.svg
:target: https://pypi.python.org/pypi/scipion-em-empiar
:alt: Supported Python versions
.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-empiar?server=https%3A%2F%2Fsonarcloud.io
:target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-empiar
:alt: SonarCloud quality gate
.. image:: https://img.shields.io/pypi/dm/scipion-em-empiar
:target: https://pypi.python.org/pypi/scipion-em-empiar
:alt: Downloads
=====
Setup
=====
In order to install the plugin follow these instructions:
1. **Install this plugin:**
.. code-block::
scipion installp -p scipion-em-empiar
or through the **plugin manager** by launching Scipion and following **Configuration** >> **Plugins**
Alternatively, in devel mode:
.. code-block::
git clone -b devel 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:
.. code-block::
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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