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