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 -i --source kipoi rbp_eclip/UPF1

predict

Run model prediction

cd ~/.kipoi/models/rbp_eclip/UPF1/example_files

kipoi predict rbp_eclip/UPF1 \
  --dataloader_args='{'intervals_file': 'intervals.bed', 'fasta_file': 'hg38_chr22.fa', 'gtf_file': 'gencode.v24.annotation_chr22.gtf'}' \
  -o '/tmp/rbp_eclip__UPF1.example_pred.tsv'

# check the results
head '/tmp/rbp_eclip__UPF1.example_pred.tsv'

test

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

kipoi test ~/.kipoi/models/rbp_eclip/UPF1/example_files

env

install

Install model dependencies

kipoi env install rbp_eclip/UPF1

create

Create a new conda environment for the model

kipoi env create rbp_eclip/UPF1
source activate kipoi-rbp_eclip__UPF

list

List all environments

kipoi env list

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