Cache to dope the result retrieval from reaction rules, to be used with RetroPath 3.0
Database based cache to dope data retrieval for RetroPath 3
Here it is a two components cache system to dope the result retrieval from reaction rules results, to be used with RetroPath 3.0. The 2 components are:
- A python module to be imported in RetroPath 3.0
- A Mongo database, which should be started independently (see "How to run the database in the background")
Notice : at reading time, some of following information might be deprecated!
- docker : https://docs.docker.com/install/
- docker-compose : https://docs.docker.com/compose/install/
- conda : https://docs.conda.io/projects/conda/en/latest/user-guide/install/
Setting up python environment
Basically: one needs a conda environment with following packages:
conda create --name myenv python=3.6 source activate myenv conda install --channel rdkit rdkit=2018.09.1.0 conda install --channel conda-forge pytest conda install pytest conda install pymongo conda install pyyaml
Install as a packages
pip install -e .
How to run the database service in the background
docker-compose -f service/run/mongo.yml up # Or 'up -d' to start in the background
- Where are stored the db files ? In a named docker data volume, see
How to cite
Please cite: to be completed
See LICENSE file
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