sibtm-variomes

A python module to retrieve relevant literature for variants-related queries

dependencies

Required Python modules:

• elasticsearch
• numpy
• pandas
• pymongo
• pysolr
• flask

Other resources:

• Requires running SIBiLS Elasticsearch and MongoDB servers
• Requires running sibtm-terminology

Python installation instructions

• Install the solr package from the sibtm-variomes directory

   pip install git+https://github.com/emilie19/sibtm-variomes.git

• Initialize the configuration file by running config.py

   python sibtmvar/microservices/init.py

• Update the configuration file for the sibtm-variomes services (~/.config/sibtm/config-variomes.ini)

   [elasticsearch]
   s_url = localhost
   i_port = <port>
   s_username = <username>
   s_password = <password>
   	
   [repository]
   r_cache = <path>/Caches/
   r_logs = <path>/Logs/
   r_errors = <path>/Errors/
   r_status = <path>/Status/
   r_api_files = <path>/API_Files/
   
   [url]
   s_mongodb = localhost:27017/
   s_synvar = http://goldorak.hesge.ch/synvar/generate/litterature/fromMutation
   s_ct = http://candy.hesge.ch/CT/CTSVIP/rankCT.jsp
  

• Update the other settings if needed in the configuration file for the sibtm-variomes services (~/.config/sibtm/config-variomes.ini)

license

This project is licensed under the terms of the GNU General Public License v3.0 license (gpl-3.0).

authors

Emilie Pasche