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Support Galaxy Expression Tools in Pulsar #263

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jmchilton opened this issue Jul 15, 2021 · 1 comment
Open

Support Galaxy Expression Tools in Pulsar #263

jmchilton opened this issue Jul 15, 2021 · 1 comment

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@jmchilton
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Need to transfer the Python script - perhaps as a config file or tool file.

@jmchilton jmchilton changed the title Support Expression Tools in Pulsar Support Galaxy Expression Tools in Pulsar Jul 15, 2021
@jmchilton
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exec_before_job writes files Pulsar doesn't know about and don't seem to respect compute environments:

        local_working_directory = param_dict["__local_working_directory__"]
        expression_inputs_path = os.path.join(local_working_directory, ExpressionTool.EXPRESSION_INPUTS_NAME)

The cd ../ is a bit questionable also.

        self.command = f"cd ../; {expressions.EXPRESSION_SCRIPT_CALL}"

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