This is a fork of https://github.com/PaoloBnn/Retip to wrap Retip to be used from Galaxy
Built images are available at https://hub.docker.com/repository/docker/recetox/retip
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
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 ...
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
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
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)
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,
conda install conda-build
conda build --R <version-of-R> .
conda install -c conda-forge --use-local r-retip