Metadata-Version: 2.1
Name: retropath2-wrapper
Version: 1.0.0
Summary: 'python wrapper to run retropath2.0 knime workflow'
Home-page: https://github.com/brsynth/retropath2-wrapper
Author: 'melchior du lac, joan hérisson'
Author-email: joan.herisson@univ-evry.fr
License: MIT
Description: # Retropath2.0 wrapper
        
        
        Implementation of the KNIME retropath2.0 workflow. Takes for input the minimal (dmin) and maximal (dmax) diameter for the reaction rules and the maximal path length (maxSteps). The tool  expects the following files: `rules.csv`, `sink.csv` and `source.csv` and produces results in an output folder.
        
        ## Standalone
        
        ### Prerequisites
        
        * Python 3
        
        ### Quick start
        The main code is `src/RetroPath2.py` and can be run as the following:
        ```
        python src/RetroPath2.py \
          -sinkfile <sink_file> \
          -sourcefile <source_file> \
          -max_steps 3 \
          -rulesfile <rules_file> \
          -topx 100 \
          -dmin 0 \
          -dmax 1000 \
          -mwmax_source 1000 \
          -mwmax_cof 1000 \
          -timeout 30 \
          -outdir <outdir_folder> \
          -is_forward False
        ```
        
        
        ## Docker
        
        RetroPath2 can be run into a docker container.
        
        ### Prerequisites
        
        * Docker - [Install](https://docs.docker.com/install/)
        
        ### Installation
        Before running the container, the image has to be built with:
        ```
        cd docker
        docker-compose build
        ```
        
        ### Run
        Then, the tool is runnable by:
        ```
        cd docker
        ./RetroPath2.sh
          -sinkfile <sink_file> \
          -sourcefile <source_file> \
          -max_steps 3 \
          -rulesfile <rules_file> \
          -topx 100 \
          -dmin 0 \
          -dmax 1000 \
          -mwmax_source 1000 \
          -mwmax_cof 1000 \
          -timeout 30 \
          -outdir <outdir_folder> \
          -is_forward False
        ```
        
        To call the tool with fresh code:
        ```
        docker-compose run --rm -v <absolutepath_to_src>:/home/src retropath2
        ```
        
        To call the tool from any location:
        ```
        cd docker
        docker-compose run --rm \
            -v <path/to/source.csv>:/home/source.csv:ro \
            -v <path/to/sink.csv>:/home/sink.csv:ro \
            -v <path/to/rules.csv>:/home/rules.csv:ro \
            -v <path/to/output_folder>:/home/outdir \
            -w /home \
            retropath2 python src/RetroPath2.py \
                -sinkfile <sink_file> \
                -sourcefile <source_file> \
                -max_steps 3 \
                -rulesfile <rules_file> \
                -topx 100 \
                -dmin 0 \
                -dmax 1000 \
                -mwmax_source 1000 \
                -mwmax_cof 1000 \
                -timeout 30 \
                -outdir <outdir_folder> \
                -is_forward False
        ```
        
        ## Test
        All modes can be tested with:
        ```
        cd test
        ./run[-in-docker].sh
        ```
        
        
        
        
        ### How to cite RetroPath2.0?
        Please cite:
        
        Delépine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering, 45: 158-170, 2018. DOI: https://doi.org/10.1016/j.ymben.2017.12.002
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.5
Description-Content-Type: text/markdown
