Command-line interface

For the command line interface the help command should explain most functionality

kipoi -h


List all models

kipoi ls


Get information on how the required dataloader keyword arguments

kipoi info Basset


Run model prediction

kipoi get-example Basset -o example
kipoi predict Basset \
  --dataloader_args='{"intervals_file": "example/intervals_file", "fasta_file": "example/fasta_file"}' \
  -o '/tmp/Basset.example_pred.tsv'
# check the results
head '/tmp/Basset.example_pred.tsv'

You can add --singularity to the command in order to execute the command in the virtual environment.


Test whether a model is defined correctly and whether is execution using the example files is successful.

kipoi test ~/.kipoi/models/Basset/example_files

In detail, kipoi test <model> checks for three things: - Whether the model specific conda environment can be created and activated successfully - Whether the data scheme that the dataloader outputs and the model expects match or not - Optionally, if there is a 'test'.'expect' field in model.yaml pointing to some *.h5 file, the predictions in the file are compared with the prediction produced by the the model. E.g.: yaml test: expect: url: md5: 1adb12be84240ffb7d7ca556eeb19e01



Create a new conda environment for the model

kipoi env create Basset
source activate kipoi-Basset


List all environments

kipoi env list

Use source activate <env> or conda activate <env> to activate the environment.

See also for more information.