mikrokondo_tools

Note

This repo is underdevelopment and not ready for routine usage

Table of Contents

• Installation
• License

Installation

Current Run Method

No package has been created yet, however the software can be run and developed using hatch. To run the tests in all supported python versions using hatch simply enter:

hatch run test:test

To run tests using a specific python version use:

# Example running using python 3.10
hatch run +py=3.10 test:test

To run the command-line options use:

hatch run +py=3.10 test:mikrokondo-tools

The above command will display command groups with help messages, and each sub command has additional help options.

pip install mikrokondo-tools

Usage

Running mikrokondo-tools generates the following help message with available options for usage:

Usage: mikrokondo-tools [OPTIONS] COMMAND [ARGS]...

Options:
  --version   Show the version and exit.
  -h, --help  Show this message and exit.

Commands:
  download     Download a database for mikrokondo
  samplesheet  Generate a sample sheet for mikrokondo.

The download option generates the following output:

Usage: mikrokondo-tools download [OPTIONS]

  Download a external file for use in mikrokondo. This script only downloads
  the file and will not untar or unzip them.

Options:
  -f, --file [gtdb-sketch|gtdb-shigella|dehost|kraken-std|bakta-light|bakta-full]
                                  Pick an option from the list to download
                                  [required]
  -o, --output PATH               An existing directory to download files to.
                                  [default: your/current/directory]
  -h, --help                      Show this message and exit.

The samplesheet option produces the following output:

Usage: mikrokondo-tools samplesheet [OPTIONS] SAMPLE_DIRECTORY

Options:
  -o, --output-sheet PATH   The file to write your created output sheet to,
                            this directory must already exist.  [required]
  -1, --read-1-suffix TEXT  A suffix to identify read 1  [default: _R1_]
  -2, --read-2-suffix TEXT  A suffix to identify read 2  [default: _R2_]
  -s, --schema-input PATH   An optional schema_input.json file pre-downloaded
                            for mikrokondo.
  -h, --help                Show this message and exit.

License

Copyright Government of Canada 2023

Written by: National Microbiology Laboratory, Public Health Agency of Canada

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this work except in compliance with the License. You may obtain a copy of the License at:

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.