ibisba/rp2paths repository overview

⁠RP2paths -- RetroPath2.0 to pathways

• Docker image: ibisba/rp2paths⁠
• Base images: conda/miniconda3/⁠ debian⁠
• Source: Dockerfile⁠, rp2paths⁠
• License: MIT License⁠ (dependencies other open source licenses)

RP2paths extracts the set of pathways that lies in a metabolic space file as outputted from the RetroPath2.0 workflow⁠

This is the Docker⁠ image and (eventually) CWL⁠ wrapping of rp2paths⁠ from Jean-Loup Faulon's group & INRA. This wrapper is maintained by IBISBA 1.0⁠, a project with funding from the European Union's Horizon 2020 research and innovation programme under grant agreement n° 730976⁠

⁠Quick start

The command line tool is accessible as rp2paths within the Docker image ibisba/rp2paths⁠ on Docker Hub.

Given a scope file rp2-results.csv in the current directory, as produced by RetroPath2.0⁠, a typical command line for extracting the pathways from the results is:

docker run -v `pwd`:/data ibisba/rp2paths 

Note that the above maps the current directory pwd to /data inside the Docker container.

The rp2paths extracts will afterwards be in the pathways/ folder:

~/examples/carotene$ ls pathways/
compounds.txt  out_discarded   out_graph2.dot  out_react
efm.err        out_efm         out_graph2.svg  out_rever
efm.log        out_full_react  out_info        reactions.erxn
img            out_graph1.dot  out_mat         sinks.txt
out_comp       out_graph1.svg  out_paths.csv

~/examples/carotene$ ls pathways/img
CMPD_0000000001.svg  CMPD_0000000008.svg  TARGET_0000000001.svg
CMPD_0000000003.svg  CMPD_0000000009.svg
CMPD_0000000004.svg  MNXM83.svg

The below example customize the rp2paths parameters, here providing /home/alice/examples/carotene as the data folder. Note that when customizing you have to provide the paths to rp2-results.csv and the output directory relative to /data:

docker run -v /home/alice/examples/carotene:/data ibisba/rp2paths ibisba/rp2paths rp2paths all rp2-results.csv --outdir pathways

where:

• all specify that all the tasks needed for retreiving pathways will be executed at once.
• rp2-results.csv is the metabolic space outputted by the RetroPath2.0 workflow.
• --outdir pathways specify the directory in which all files will be outputted (here /data/pathways in the container, aka /home/alice/examples/carotene/pathways on the host).

In the output folder (here pathways), the complete set of pathways enumerated will be written in the out_paths.csv file. In addition, for each pathway there will be a .dot file (.dot representation of the graph) and a .svg file (.svg depiction of the pathway).

Additional options are described in the embedded help

docker run ibisba/rp2paths rp2paths --help
docker run ibisba/rp2paths rp2paths all --help

⁠Contributing

To build the docker image yourself, use

docker build -t ibisba/rp2paths .

You may test the Docker image locally, replicating what is run automatically by Travis CI⁠:

./test.sh

To contribute fixes to this Docker/CWL wrapping, raise a issue⁠ or pull request⁠

For improvements on rp2paths⁠ itself you may raise an issues⁠ or pull request⁠

Contributions are assumed to be covered by the MIT license⁠.

⁠How to cite RP2paths?

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

⁠Licence

RP2paths, the Dockerfile, examples and cwl tool descriptions are released under the MIT licence. See the LICENCE.txt⁠ file for details.

The Docker image contains software dependencies under other open source licenses. Notably:

• debian⁠: GNU GPL and others⁠
• conda/miniconda3⁠: BSD 3-clause and others⁠
• rdkit⁠: BSD 3-clause⁠
• openjdk-8⁠: GNU GPL 2 with classpath exception⁠
• python3⁠: PSF and others⁠