Version of run_tool exercise for discussion #6
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nsoranzo
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Jul 17, 2020
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Thanks a lot @claresloggett ! I was thinking, maybe the tool search/view/run part could be put in a separate exercise?
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "sort_tool = 'sort1'" |
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| "sort_tool = 'sort1'" | |
| "sort_tool_id = 'sort1'" |
| } | ||
| ], | ||
| "source": [ | ||
| "tool_details = tc.show_tool(sort_tool, io_details=True)\n", |
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| "tool_details = tc.show_tool(sort_tool, io_details=True)\n", | |
| "tool_details = tc.show_tool(sort_tool_id, io_details=True)\n", |
| } | ||
| ], | ||
| "source": [ | ||
| "tc.run_tool(new_hist['id'], sort_tool,\n", |
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| "tc.run_tool(new_hist['id'], sort_tool,\n", | |
| "gi.tools.run_tool(new_hist['id'], sort_tool_id,\n", |
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "9) Create a `bioblend.galaxy.tools.ToolClient` object." |
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To make it simpler I tend to use gi.tools instead of creating separate objects.
| } | ||
| ], | ||
| "source": [ | ||
| "pprint(tc.get_tools(name='Sort'))" |
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| "pprint(tc.get_tools(name='Sort'))" | |
| "pprint(gi.tools.get_tools(name='Sort'))" |
| @@ -339,7 +347,522 @@ | |||
| "cell_type": "markdown", | |||
| "metadata": {}, | |||
| "source": [ | |||
| "8) View the results on the Galaxy server with your web browser." | |||
| "8) Get the id of the output dataset from the workflow. You can get this from the history, or by getting the job id from `gi.workflows.show_invocation()` and then the output dataset id from the job using `gi.jobs.show_job()`. You'll need to wait until the workflow jobs have been scheduled." | |||
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| "8) Get the id of the output dataset from the workflow. You can get this from the history, or by getting the job id from `gi.workflows.show_invocation()` and then the output dataset id from the job using `gi.jobs.show_job()`. You'll need to wait until the workflow jobs have been scheduled." | |
| "8) Get the id of the output dataset from the workflow. You can get this from the history, or by getting first the job id from `gi.invocations.show_invocation()`, and then the output dataset id from the job using `gi.jobs.show_job()`. You will need to wait until the workflow jobs have been scheduled." |
| } | ||
| ], | ||
| "source": [ | ||
| "invocation = gi.workflows.show_invocation(wf['id'],ret['id'])\n", |
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| "invocation = gi.workflows.show_invocation(wf['id'],ret['id'])\n", | |
| "invocation = gi.invocations.show_invocation(ret['id'])\n", |
It would be probably good to replace ret with something like invocation or wf_inv here and above.
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "11) Check the tool inputs by calling `show_tool()` with `io_details=True`. It might be useful to open Galaxy and compare the inputs you see here to the tool inputs in the Galaxy UI." |
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| "11) Check the tool inputs by calling `show_tool()` with `io_details=True`. It might be useful to open Galaxy and compare the inputs you see here to the tool inputs in the Galaxy UI." | |
| "11) Inspect the tool inputs by calling `show_tool()` with `io_details=True`. It might be useful to open Galaxy and compare the inputs you see here to the tool inputs in the Galaxy UI." |
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Some exercises added to the bioblend API notebook for discussion. For now just added to the ex1_bioblend_answers notebook; the exercises notebook hasn't been updated.
The basic idea is to get the output dataset from the workflow (i.e. the tabular dataset) and sort it using
run_tool().I think this may be too much, particularly for the upcoming conference where teaching might be slow. Some steps, like getting the output dataset, are a bit fiddly. Do we want this stuff in now? Or can it be simplified?