Command-line interface

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

kipoi -h

ls

List all models

kipoi ls

info

Get information on how the required dataloader keyword arguments

kipoi info Basset

predict

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

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

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

env

install

Install model dependencies

kipoi env install Basset

create

Create a new conda environment for the model

kipoi env create Basset
source activate kipoi-Basset

list

List all environments

kipoi env list

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

See also https://github.com/kipoi/examples for more information.