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.
Setup
In order to install the plugin follow these instructions:
Install this plugin:
scipion installp -p scipion-em-empiaror through the plugin manager by launching Scipion and following Configuration >> Plugins
Alternatively, in devel mode:
git clone -b devel https://github.com/scipion-em/scipion-em-empiar.git
scipion installp -p local/path/to/scipion-em-empiar --develDownload 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>
Release files for scipion-em-empiar 3.1.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| scipion-em-empiar-3.1.1.tar.gz | 47.3 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scipion_em_empiar-3.1.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 96.0 kB
Release files / scipion-em-empiar-3.1.1.tar.gz
| Download URL | scipion-em-empiar-3.1.1.tar.gz |
|---|---|
| Size | 47.3 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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|
|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.8.18
|
Release files / scipion_em_empiar-3.1.1-py3-none-any.whl
| Download URL | scipion_em_empiar-3.1.1-py3-none-any.whl |
|---|---|
| Size | 48.7 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
b2781afb6c610cda1bec82b115e8e0b37160f73ef2da8d18ec32dcbf0a6bbd7f
|
|
BLAKE2b-256 checksum How to use checksums |
3b106b873b349ea14a20aa0078265cf06492f57cf6b9a80ae0791c614e835f80
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.8.18
|
