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Below are some examples of common actions that can be carried out via the Command-line Agent.
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List available accounts
epi2me accounts list
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Describe a workflow (show details):
epi2me workflows detail $WORKFLOW_ID
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Run new analysis (interactive mode)
This is analogous to starting a new analysis in EPI2ME where the user is interactively led through the process. The command to run in interactive mode takes the following form:
epi2me workflows run $INPUT_1 ... $INPUT_N
Here is a screenshot of a new analysis that was started interactively where the user is able to modify the settings at every step as they would in the Desktop Agent:
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Run new analysis (non-human data and accept defaults)
- Multiple data sources as input
- Data sources contain no human data
epi2me workflows run $INPUT_1 ... $INPUT_N --nothuman --workflow $WORKFLOW_ID --account $ACCOUNT_NUMBER
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Run new analysis (human data with project tagging and opt-in storage. Accept defaults for the rest)
epi2me workflows run $INPUT_1 ... $INPUT_N --consentedHuman --workflow $WORKFLOW_ID --account $ACCOUNT_NUMBER --output $OUTPUT_LOCATION --store --quiet