Purpose

This is a fork of https://github.com/PaoloBnn/Retip to wrap Retip to be used from Galaxy

Images

Built images are available at https://hub.docker.com/repository/docker/recetox/retip

Build

docker build -t CONTAINER/NAME:TAG .

Downloads https://github.com/PaoloBnn/Retiplib, picks Retip code from here, adds all necessary dependencies and builds everything in a container.

Bioconda build is planned, not working yet

Usage

Helper scripts galaxy/*.R invoke the library, they are intended to be executed with Rscript in the cotainer, wrapped in Galaxy tools.

For testing etc., standalone invocation is:

$ cd /where/your/data/are
$ docker run -u $(id -u) -w /work -v $PWD:/work CONTAINER/NAME:TAG SCRIPT.R ARGS ...

Compute chemical descriptors

chemdesc.R compounds.tsv descriptors.feather

Input: compounds.tsv is a table with columns Name, InChIKey, SMILES, RT

Output: descriptors.feather, table of RDKIT chemical descriptors, to be used as input to the other tools

Train Keras model

trainKeras.R descriptors.feather model.hdf5 

Input: descriptors.feather -- set of the descriptors and RTs, as produced by chemdesc.R Output: model.hdf5 -- trained model

Apply the Keras model to a single SMILES

spell.R descriptors.feather model.hdf5 input.tsv output.tsv

Inputs:descriptors.feather -- the same file that was used to train Keras; model.hdf5 -- output of trainKeras.R, SMILES the formula Output: output.tsv (with predictions)

Testing data

In galaxy/examples/:

• compounds.tsv: converted from original examples/Plasma_positive.xlsx, 494 records, takes some time to process
• compounds-small.tsv: first 80 lines of the original example, just few minutes test run
• compounds-tiny.tsv: just few lines,

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Quickstart (original)

conda install conda-build
conda build --R <version-of-R> .
conda install -c conda-forge --use-local r-retip