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https://github.com/brsynth/retropath2-wrapper

Python wrapper for Retropath2.0 Knime workflow

https://github.com/brsynth/retropath2-wrapper

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.3%) to scientific vocabulary

Keywords

metabolic-engineering synbio synthetic-biology
Last synced: 6 months ago · JSON representation

Repository

Python wrapper for Retropath2.0 Knime workflow

Basic Info
  • Host: GitHub
  • Owner: brsynth
  • License: mit
  • Language: JavaScript
  • Default Branch: master
  • Homepage:
  • Size: 72.9 MB
Statistics
  • Stars: 8
  • Watchers: 3
  • Forks: 1
  • Open Issues: 3
  • Releases: 18
Topics
metabolic-engineering synbio synthetic-biology
Created almost 6 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License Authors

README.md

Retropath2.0 Python wrapper

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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.

Prerequisites

  • Python 3
  • KNIME (code was tested on 4.6.4, 4.7.0 versions)

Install

Prerequisite

The conda package manager is required. Fresh instructions on how to install conda are available online.

The tool tries to install the KNIME Anlytical Platform as well as the RetroPath2.0 node dependancies.

conda package

Install in the <my_env> conda environment: shell conda install -c conda-forge -n <my_env> retropath2_wrapper

Run

Disclaimer: we recommand to provide absolute path to files, problems can arise with relative paths.

From CLI (Linux, macOS)

sh python -m retropath2_wrapper <sink-file> <rules-file> <out-dir> --source_file <source-file>

From Python code

The minimal required arguments are sink_file, source_file, rules_file and outdir. ```python from retropath2_wrapper import retropath2

rcode = retropath2( sinkfile='/path/to/sink/file', sourcefile='/path/to/source/file', rulesfile='/path/to/rules/file', outdir='/path/to/outdir' ) ```

Exploration settings have default values and can be tuned: ```python from retropath2_wrapper import retropath2

rcode = retropath2( sinkfile='/path/to/sink/file', sourcefile='/path/to/source/file', rulesfile='/path/to/rules/file', outdir='/path/to/outdir', maxsteps=3, topx=100, dmin=0, dmax=100, mwmaxsource=1000, ) ```

Already installed KNIME app can hence be used that way, eg: ```python from retropath2_wrapper import retropath2

rcode = retropath2( sinkfile='/path/to/sink/file', sourcefile='/path/to/source/file', rulesfile='/path/to/rules/file', outdir='/path/to/outdir' kexec='/Applications/KNIME 4.3.0.app/Contents/MacOS/knime', ) ```

Executions can be timed out using the timeout arguments (in minutes).

Return codes

retropath2() function returns one of the following codes: * 0: No error * 1: File is not found * 2: Running the RetroPath2.0 Knime program produced an OSError * 3: InChI is malformated * 10: Source has been found in the sink (warning) * 11: No solution is found (warning)

Tests

Test can be run with the following commands:

Natively

sh conda install -c conda-forge pytest python -m pytest tests

To run functional tests, the environment variable RP2_FUNCTIONAL=TRUE is required.

Knime dependencies

Two options are available: 1. You provide a path of the Knime executable through the argument --kexec. You need to have the following libraries installed: org.knime.features.chem.types.feature.group, org.knime.features.datageneration.feature.group, org.knime.features.python.feature.group, org.rdkit.knime.feature.feature.group 2. retropath2_wrapper will install Knime for you by downloading the softwares available on Zenodo. You can choose a version among 4.6.4 or 4.7.0. Optionally, you can locate a path for the installation. If an executable is found in the path, Knime will not be reinstalled.

Knime software and packages are available at: * KNIME * KNIME v4.6.4 - Zenodo * KNIME v4.7.0 - Zenodo

Known issues

  1. Could not load native RDKit library, libfreetype.so.6: cannot open shared object file Some Knime versions (like: 4.3.0) or environments can't load RDKit library. You need to append the $CONDA_PREFIX/lib path to the LD_LIBRARY_PATH variable where the libfreetype library is available: sh conda activate <env_name> export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$CONDA_PREFIX/lib"

CI/CD

For further tests and development tools, a CI toolkit is provided in cicd-toolkit folder (see cicd-toolkit/README.md).

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

Owner

  • Name: BioRetroSynth
  • Login: brsynth
  • Kind: organization

Our group is interested in synthetic biology and systems metabolic engineering in whole-cell and cell-free systems.

GitHub Events

Total
  • Release event: 2
  • Watch event: 1
  • Push event: 12
  • Pull request event: 3
  • Create event: 3
Last Year
  • Release event: 2
  • Watch event: 1
  • Push event: 12
  • Pull request event: 3
  • Create event: 3

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 370
  • Total Committers: 3
  • Avg Commits per committer: 123.333
  • Development Distribution Score (DDS): 0.127
Top Committers
Name Email Commits
joan j****n@u****r 323
Guillaume Gricourt g****i@g****m 28
Thomas Duigou t****u@i****r 19
Committer Domains (Top 20 + Academic)
inrae.fr: 1 univ-evry.fr: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 10
  • Total pull requests: 9
  • Average time to close issues: 4 months
  • Average time to close pull requests: 28 days
  • Total issue authors: 7
  • Total pull request authors: 2
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.22
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 6 months
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
  • tduigou (3)
  • guillaume-gricourt (2)
  • niraito (1)
  • bbanzai88 (1)
  • cn-lugen (1)
  • Abdel-youssef (1)
  • razmarques (1)
Pull Request Authors
  • guillaume-gricourt (9)
  • dependabot[bot] (1)
Top Labels
Issue Labels
Pull Request Labels
bug (1) dependencies (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 34 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 11
  • Total maintainers: 1
pypi.org: retropath2-wrapper

'python wrapper to run retropath2.0 knime workflow'

  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 34 Last month
  • Docker Downloads: 0
Rankings
Docker downloads count: 4.2%
Dependent packages count: 10.0%
Average: 19.1%
Stargazers count: 20.3%
Dependent repos count: 21.7%
Downloads: 28.5%
Forks count: 29.8%
Maintainers (1)
breakthewall
Last synced: 6 months ago

Dependencies

.github/workflows/check.yml actions
  • actions/checkout v2 composite
  • docker://continuumio/miniconda3 * composite
.github/workflows/tag.yml actions
  • actions/checkout v2 composite
  • actions/create-release v1 composite
  • actions/download-artifact v2 composite
  • actions/upload-artifact v2 composite
  • ad-m/github-push-action master composite
  • conda-incubator/setup-miniconda v2 composite
  • mathieudutour/github-tag-action v5.6 composite
  • ruby/setup-ruby v1 composite
.github/workflows/test.yml actions
  • actions/checkout v2 composite
  • conda-incubator/setup-miniconda v2 composite
setup.py pypi
environment.yaml pypi