Create a full command line executable workflow for RNA-Seq on PBMC Samples. Open a new pull request (on a separate branch) and comment the PR number here when you're done.

[KastanDay]

Experiment Type: RNA-Seq Sequencing of total cellular RNA

Workflow Management: Bash/SLURM Scripting and job scheduling

Software Stack: FastQC MultiQC STAR RSEM samtools DESeq2

What else to know about the pipeline? I am working PBMC samples collected from patients that are undergoing immunotherapy.

Use the data files existing in Report_WholeBrain as input for this workflow.

You should write a series of bash scripts and R scripts that can accomplish this task. Open a PR with those scripts when you're done.

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Error in handle_issue_opened: 'OPENAI_API_TYPE' Traceback

Traceback (most recent call last):
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/ai_ta_backend/agents/github_webhook_handlers.py", line 90, in handle_issue_opened
    bot = WorkflowAgent(run_id_in_metadata=langsmith_run_id)
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 23, in __init__
    if os.environ['OPENAI_API_TYPE'] == 'azure':
  File "/usr/local/Cellar/python@3.10/3.10.13/Frameworks/Python.framework/Versions/3.10/lib/python3.10/os.py", line 680, in __getitem__
    raise KeyError(key) from None
KeyError: 'OPENAI_API_TYPE'

[lil-jr-dev[bot]]

Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review.

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Error in handle_issue_opened: 1 validation error for AzureChatOpenAI root Did not find openai_api_base, please add an environment variable OPENAI_API_BASE which contains it, or pass openai_api_base as a named parameter. (type=value_error) Traceback

Traceback (most recent call last):
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/ai_ta_backend/agents/github_webhook_handlers.py", line 90, in handle_issue_opened
    bot = WorkflowAgent(run_id_in_metadata=langsmith_run_id)
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 24, in __init__
    self.llm = AzureChatOpenAI(temperature=0, model="gpt-4-0613", max_retries=3, request_timeout=60 * 3, deployment_name=os.environ['AZURE_OPENAI_ENGINE'])  # type: ignore
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/load/serializable.py", line 97, in __init__
    super().__init__(**kwargs)
  File "pydantic/main.py", line 341, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for AzureChatOpenAI
__root__
  Did not find openai_api_base, please add an environment variable `OPENAI_API_BASE` which contains it, or pass  `openai_api_base` as a named parameter. (type=value_error)

[lil-jr-dev[bot]]

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[lil-jr-dev[bot]]

Error in handle_issue_opened: Executable doesn't exist at /Users/rohanmarwaha/Library/Caches/ms-playwright/chromium-1084/chrome-mac/Chromium.app/Contents/MacOS/Chromium ╔════════════════════════════════════════════════════════════╗ ║ Looks like Playwright was just installed or updated. ║ ║ Please run the following command to download new browsers: ║ ║ ║ ║ playwright install ║ ║ ║ ║ <3 Playwright Team ║ ╚════════════════════════════════════════════════════════════╝ Traceback

Traceback (most recent call last):
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/ai_ta_backend/agents/github_webhook_handlers.py", line 90, in handle_issue_opened
    bot = WorkflowAgent(run_id_in_metadata=langsmith_run_id)
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 27, in __init__
    self.agent = self.make_agent()
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 39, in make_agent
    tools = get_tools(self.llm, sync=True)
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/ai_ta_backend/agents/tools.py", line 43, in get_tools
    sync_browser = create_sync_playwright_browser()
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/tools/playwright/utils.py", line 82, in create_sync_playwright_browser
    return browser.chromium.launch(headless=headless)
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/sync_api/_generated.py", line 14778, in launch
    self._sync(
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/_impl/_sync_base.py", line 109, in _sync
    return task.result()
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/_impl/_browser_type.py", line 96, in launch
    Browser, from_channel(await self._channel.send("launch", params))
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/_impl/_connection.py", line 61, in send
    return await self._connection.wrap_api_call(
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/_impl/_connection.py", line 490, in wrap_api_call
    return await cb()
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/_impl/_connection.py", line 99, in inner_send
    result = next(iter(done)).result()
playwright._impl._api_types.Error: Executable doesn't exist at /Users/rohanmarwaha/Library/Caches/ms-playwright/chromium-1084/chrome-mac/Chromium.app/Contents/MacOS/Chromium
╔════════════════════════════════════════════════════════════╗
║ Looks like Playwright was just installed or updated.       ║
║ Please run the following command to download new browsers: ║
║                                                            ║
║     playwright install                                     ║
║                                                            ║
║ <3 Playwright Team                                         ║
╚════════════════════════════════════════════════════════════╝

[lil-jr-dev[bot]]

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[lil-jr-dev[bot]]

Error in handle_issue_opened: Executable doesn't exist at /Users/kastanday/Library/Caches/ms-playwright/chromium-1084/chrome-mac/Chromium.app/Contents/MacOS/Chromium ╔════════════════════════════════════════════════════════════╗ ║ Looks like Playwright was just installed or updated. ║ ║ Please run the following command to download new browsers: ║ ║ ║ ║ playwright install ║ ║ ║ ║ <3 Playwright Team ║ ╚════════════════════════════════════════════════════════════╝ Traceback

Traceback (most recent call last):
  File "/Users/kastanday/code/ncsa/ai-ta/ai-ta-backend/ai_ta_backend/agents/github_webhook_handlers.py", line 90, in handle_issue_opened
    bot = WorkflowAgent(run_id_in_metadata=langsmith_run_id)
  File "/Users/kastanday/code/ncsa/ai-ta/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 30, in __init__
    self.agent = self.make_agent()
  File "/Users/kastanday/code/ncsa/ai-ta/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 41, in make_agent
    tools = get_tools(self.llm, sync=True)
  File "/Users/kastanday/code/ncsa/ai-ta/ai-ta-backend/ai_ta_backend/agents/tools.py", line 43, in get_tools
    sync_browser = create_sync_playwright_browser()
  File "/Users/kastanday/miniforge3/envs/flask10_py10/lib/python3.10/site-packages/langchain/tools/playwright/utils.py", line 82, in create_sync_playwright_browser
    return browser.chromium.launch(headless=headless)
  File "/Users/kastanday/miniforge3/envs/flask10_py10/lib/python3.10/site-packages/playwright/sync_api/_generated.py", line 14778, in launch
    self._sync(
  File "/Users/kastanday/miniforge3/envs/flask10_py10/lib/python3.10/site-packages/playwright/_impl/_sync_base.py", line 109, in _sync
    return task.result()
  File "/Users/kastanday/miniforge3/envs/flask10_py10/lib/python3.10/site-packages/playwright/_impl/_browser_type.py", line 96, in launch
    Browser, from_channel(await self._channel.send("launch", params))
  File "/Users/kastanday/miniforge3/envs/flask10_py10/lib/python3.10/site-packages/playwright/_impl/_connection.py", line 61, in send
    return await self._connection.wrap_api_call(
  File "/Users/kastanday/miniforge3/envs/flask10_py10/lib/python3.10/site-packages/playwright/_impl/_connection.py", line 490, in wrap_api_call
    return await cb()
  File "/Users/kastanday/miniforge3/envs/flask10_py10/lib/python3.10/site-packages/playwright/_impl/_connection.py", line 99, in inner_send
    result = next(iter(done)).result()
playwright._impl._api_types.Error: Executable doesn't exist at /Users/kastanday/Library/Caches/ms-playwright/chromium-1084/chrome-mac/Chromium.app/Contents/MacOS/Chromium
╔════════════════════════════════════════════════════════════╗
║ Looks like Playwright was just installed or updated.       ║
║ Please run the following command to download new browsers: ║
║                                                            ║
║     playwright install                                     ║
║                                                            ║
║ <3 Playwright Team                                         ║
╚════════════════════════════════════════════════════════════╝

[lil-jr-dev[bot]]

Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review.

You can monitor the LangSmith trace here.

Feel free to comment in this thread to give me additional instructions, or I'll tag you in a comment if I get stuck. If I think I'm successful I'll 'request your review' on the resulting PR. Just watch for emails while I work.

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