Table of Contents
The easiest way to install the repository is from pip by running the following command.
pip install mikrokondo-tools
conda install mikrokondo-tools -c bioconda
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.
This option can be used to create a developer install from the source repository.
pip install -e mikrokondo-toolsRunning 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 command can be used to create and validate sample sheet from a directory of NGS data. The schema_input.json file is downloaded directly from the main mikrokondo repository each time so this utility will update with the pipeline. You can still pass a pre-existing schema_input.json file to the utility if you do not have internet access or you are using an older version of the pipeline that is no longer supported.
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.
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.