Implement an RNA-Sequence Analysis Workflow using DESEQ2. Open a new pull request on a separate branch and comment the PR number here when you're done.

[KastanDay]

Implement RNA-Sequence Analysis Workflow as per the following steps.

Quality assess and clean raw sequencing data Align reads to a reference Count the number of reads assigned to each contig/gene Extract counts and store in a matrix Create column metadata table Analyze count data using DESEQ2 Please write and execute the code to do DESEQ2 analysis on the data. If you generate results, please push them to github and mention that in your pull request. Make sure you execute the code, and if it fails keep re-trying with improvements until you get something useful to share.

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Error in handle_issue_opened: API key is required, please visit https://e2b.dev/docs to get your API key. You can either set the environment variable E2B_API_KEY or you can pass it directly to the sandbox like Sandbox(apikey="e2b...") Traceback

Traceback (most recent call last):
  File "/app/ai_ta_backend/agents/github_webhook_handlers.py", line 157, in handle_issue_opened
    bot = WorkflowAgent(langsmith_run_id=langsmith_run_id)
  File "/app/ai_ta_backend/agents/ml4bio_agent.py", line 31, in __init__
    self.agent = self.make_agent()
  File "/app/ai_ta_backend/agents/ml4bio_agent.py", line 41, in make_agent
    tools = get_tools(langsmith_run_id=self.langsmith_run_id)
  File "/app/ai_ta_backend/agents/tools.py", line 38, in get_tools
    code_execution_class = E2B_class(langsmith_run_id=langsmith_run_id)
  File "/app/ai_ta_backend/agents/code_intrepreter_sanbox.py", line 19, in __init__
    self.sandbox = Sandbox(env_vars=env_vars)
  File "/opt/venv/lib/python3.10/site-packages/e2b/sandbox/main.py", line 126, in __init__
    super().__init__(
  File "/opt/venv/lib/python3.10/site-packages/e2b/sandbox/sandbox_connection.py", line 104, in __init__
    api_key = get_api_key(api_key)
  File "/opt/venv/lib/python3.10/site-packages/e2b/utils/api_key.py", line 11, in get_api_key
    raise AuthenticationException(
e2b.sandbox.exception.AuthenticationException: API key is required, please visit https://e2b.dev/docs to get your API key. You can either set the environment variable `E2B_API_KEY` or you can pass it directly to the sandbox like Sandbox(api_key="e2b_...")

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

Traceback (most recent call last):
  File "/app/ai_ta_backend/agents/github_webhook_handlers.py", line 157, in handle_issue_opened
    bot = WorkflowAgent(langsmith_run_id=langsmith_run_id)
  File "/app/ai_ta_backend/agents/ml4bio_agent.py", line 31, in __init__
    self.agent = self.make_agent()
  File "/app/ai_ta_backend/agents/ml4bio_agent.py", line 41, in make_agent
    tools = get_tools(langsmith_run_id=self.langsmith_run_id)
  File "/app/ai_ta_backend/agents/tools.py", line 78, in get_tools
    search = load_tools(["serpapi"])
  File "/opt/venv/lib/python3.10/site-packages/langchain/agents/load_tools.py", line 611, in load_tools
    tool = _get_tool_func(**sub_kwargs)
  File "/opt/venv/lib/python3.10/site-packages/langchain/agents/load_tools.py", line 301, in _get_serpapi
    func=SerpAPIWrapper(**kwargs).run,
  File "pydantic/main.py", line 341, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for SerpAPIWrapper
__root__
  Did not find serpapi_api_key, please add an environment variable `SERPAPI_API_KEY` which contains it, or pass `serpapi_api_key` as a named parameter. (type=value_error)

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Error in handle_issue_opened: 1 validation error for SerpAPIWrapper root Could not import serpapi python package. Please install it with pip install google-search-results. (type=value_error) Traceback

Traceback (most recent call last):
  File "/app/ai_ta_backend/agents/github_webhook_handlers.py", line 157, in handle_issue_opened
    bot = WorkflowAgent(langsmith_run_id=langsmith_run_id)
  File "/app/ai_ta_backend/agents/ml4bio_agent.py", line 31, in __init__
    self.agent = self.make_agent()
  File "/app/ai_ta_backend/agents/ml4bio_agent.py", line 41, in make_agent
    tools = get_tools(langsmith_run_id=self.langsmith_run_id)
  File "/app/ai_ta_backend/agents/tools.py", line 78, in get_tools
    search = load_tools(["serpapi"])
  File "/opt/venv/lib/python3.10/site-packages/langchain/agents/load_tools.py", line 611, in load_tools
    tool = _get_tool_func(**sub_kwargs)
  File "/opt/venv/lib/python3.10/site-packages/langchain/agents/load_tools.py", line 301, in _get_serpapi
    func=SerpAPIWrapper(**kwargs).run,
  File "pydantic/main.py", line 341, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for SerpAPIWrapper
__root__
  Could not import serpapi python package. Please install it with `pip install google-search-results`. (type=value_error)

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Error in handle_issue_opened: 'CallbackManager' object has no attribute 'raise_error' Traceback

Traceback (most recent call last):
  File "/opt/venv/lib/python3.10/site-packages/langchain_core/callbacks/manager.py", line 255, in handle_event
    if ignore_condition_name is None or not getattr(
AttributeError: 'CallbackManager' object has no attribute 'ignore_chain'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/app/ai_ta_backend/agents/github_webhook_handlers.py", line 158, in handle_issue_opened
    result = bot.run(prompt)
  File "/app/ai_ta_backend/agents/ml4bio_agent.py", line 34, in run
    result = self.agent.with_config({"run_name": "ML4BIO Plan & Execute Agent"}).invoke({"input":f"{input}"}, {"metadata": {"langsmith_run_id": str(self.langsmith_run_id)}})
  File "/opt/venv/lib/python3.10/site-packages/langchain_core/runnables/base.py", line 4064, in invoke
    return self.bound.invoke(
  File "/opt/venv/lib/python3.10/site-packages/langchain/chains/base.py", line 162, in invoke
    raise e
  File "/opt/venv/lib/python3.10/site-packages/langchain/chains/base.py", line 156, in invoke
    self._call(inputs, run_manager=run_manager)
  File "/opt/venv/lib/python3.10/site-packages/langchain_experimental/plan_and_execute/agent_executor.py", line 56, in _call
    response = self.executor.step(
  File "/opt/venv/lib/python3.10/site-packages/langchain_experimental/plan_and_execute/executors/base.py", line 37, in step
    response = self.chain.run(**inputs, callbacks=callbacks)
  File "/opt/venv/lib/python3.10/site-packages/langchain_core/_api/deprecation.py", line 145, in warning_emitting_wrapper
    return wrapped(*args, **kwargs)
  File "/opt/venv/lib/python3.10/site-packages/langchain/chains/base.py", line 543, in run
    return self(kwargs, callbacks=callbacks, tags=tags, metadata=metadata)[
  File "/opt/venv/lib/python3.10/site-packages/langchain_core/_api/deprecation.py", line 145, in warning_emitting_wrapper
    return wrapped(*args, **kwargs)
  File "/opt/venv/lib/python3.10/site-packages/langchain/chains/base.py", line 363, in __call__
    return self.invoke(
  File "/opt/venv/lib/python3.10/site-packages/langchain/chains/base.py", line 162, in invoke
    raise e
  File "/opt/venv/lib/python3.10/site-packages/langchain/chains/base.py", line 156, in invoke
    self._call(inputs, run_manager=run_manager)
  File "/opt/venv/lib/python3.10/site-packages/langchain/agents/agent.py", line 1391, in _call
    next_step_output = self._take_next_step(
  File "/opt/venv/lib/python3.10/site-packages/langchain/agents/agent.py", line 1097, in _take_next_step
    [
  File "/opt/venv/lib/python3.10/site-packages/langchain/agents/agent.py", line 1097, in <listcomp>
    [
  File "/opt/venv/lib/python3.10/site-packages/langchain/agents/agent.py", line 1182, in _iter_next_step
    yield self._perform_agent_action(
  File "/opt/venv/lib/python3.10/site-packages/langchain/agents/agent.py", line 1204, in _perform_agent_action
    observation = tool.run(
  File "/opt/venv/lib/python3.10/site-packages/langchain_core/tools.py", line 401, in run
    raise e
  File "/opt/venv/lib/python3.10/site-packages/langchain_core/tools.py", line 358, in run
    self._run(*tool_args, run_manager=run_manager, **tool_kwargs)
  File "/opt/venv/lib/python3.10/site-packages/langchain_community/tools/vectorstore/tool.py", line 57, in _run
    return chain.invoke(
  File "/opt/venv/lib/python3.10/site-packages/langchain/chains/base.py", line 149, in invoke
    run_manager = callback_manager.on_chain_start(
  File "/opt/venv/lib/python3.10/site-packages/langchain_core/callbacks/manager.py", line 1296, in on_chain_start
    handle_event(
  File "/opt/venv/lib/python3.10/site-packages/langchain_core/callbacks/manager.py", line 285, in handle_event
    if handler.raise_error:
AttributeError: 'CallbackManager' object has no attribute 'raise_error'

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