Usage
Using as a command line interface¶
This is the main intention of BGCFlow wrapper usage.
Overview¶
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Typical Usage¶
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The first step of using BGCFlow wrapper is to get a copy (or clone) of the main BGCFlow Snakemake workflow.
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# get a clone of BGCFlow in your local machine bgcflow clone MY_BGCFLOW_PATH #change PATH accordingly
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Then, initiate a project config by:
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# initiate an example config and projects from template bgcflow init --bgcflow_dir MY_BGCFLOW_PATH
This will generate a file called
config.yaml
in theconfig/
folder inside the cloned BGCFlow directory -
Once the config files are set, we can do a snakemake dry-run:
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# do a dry-run bgcflow run -n --bgcflow_dir MY_BGCFLOW_PATH
While the workflow is running, the command automatically serve
Panoptes-UI
atlocalhost:5000
` to monitor jobs. -
To find out all the rules that can be added in the configuration file, do:
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# find out available rules bgcflow rules --bgcflow_dir MY_BGCFLOW_PATH
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To get more details about each individual rules, do:
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# get description of a rule bgcflow rules --describe antismash --bgcflow_dir MY_BGCFLOW_PATH/
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To find out how to cite each rules, do:
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# get citation of a rule bgcflow rules --cite antismash --bgcflow_dir MY_BGCFLOW_PATH/
Using as a python library¶
You can also generate new projects via python or Jupyter notebooks:
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