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KastanDay / ML4Bio

LLMs to execute Bioinformatics workflows, esp. RNA-seq
MIT License
0 stars 1 forks source link

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. #19

Open rohan-uiuc opened 1 year ago

rohan-uiuc commented 1 year ago

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.

lil-jr-dev[bot] commented 1 year ago

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.

lil-jr-dev[bot] commented 1 year ago

Error in handle_issue_opened: list index out of range Traceback

Traceback (most recent call last):
  File "/app/utils.py", line 69, in fancier_trim_intermediate_steps
    log = Log(message=f"trim_intermediate_steps",
NameError: name 'Log' is not defined

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/app/github_webhook_handlers.py", line 96, in handle_issue_opened
    result = bot.run(prompt)
  File "/app/ml4bio_agent.py", line 34, in run
    result = self.agent.with_config({"run_name": "ML4BIO Plan & Execute Agent"}).invoke({"input":f"{input}"}, {"metadata": {"run_id_in_metadata": str(self.run_id_in_metadata)}})
  File "/usr/local/lib/python3.10/dist-packages/langchain/schema/runnable/base.py", line 2316, in invoke
    return self.bound.invoke(
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 84, in invoke
    return self(
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 306, in __call__
    raise e
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 300, in __call__
    self._call(inputs, run_manager=run_manager)
  File "/usr/local/lib/python3.10/dist-packages/langchain_experimental/plan_and_execute/agent_executor.py", line 56, in _call
    response = self.executor.step(
  File "/usr/local/lib/python3.10/dist-packages/langchain_experimental/plan_and_execute/executors/base.py", line 37, in step
    response = self.chain.run(**inputs, callbacks=callbacks)
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 506, in run
    return self(kwargs, callbacks=callbacks, tags=tags, metadata=metadata)[
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 306, in __call__
    raise e
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 300, in __call__
    self._call(inputs, run_manager=run_manager)
  File "/usr/local/lib/python3.10/dist-packages/langchain/agents/agent.py", line 1141, in _call
    next_step_output = self._take_next_step(
  File "/usr/local/lib/python3.10/dist-packages/langchain/agents/agent.py", line 925, in _take_next_step
    intermediate_steps = self._prepare_intermediate_steps(intermediate_steps)
  File "/usr/local/lib/python3.10/dist-packages/langchain/agents/agent.py", line 1258, in _prepare_intermediate_steps
    return self.trim_intermediate_steps(intermediate_steps)
  File "/app/utils.py", line 84, in fancier_trim_intermediate_steps
    return [steps[-1]]
IndexError: list index out of range
lil-jr-dev[bot] commented 1 year ago

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.

lil-jr-dev[bot] commented 1 year ago

Error in handle_issue_opened: list index out of range Traceback

Traceback (most recent call last):
  File "/app/utils.py", line 69, in fancier_trim_intermediate_steps
    log = Log(message=f"trim_intermediate_steps",
NameError: name 'Log' is not defined

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/app/github_webhook_handlers.py", line 96, in handle_issue_opened
    result = bot.run(prompt)
  File "/app/ml4bio_agent.py", line 34, in run
    result = self.agent.with_config({"run_name": "ML4BIO Plan & Execute Agent"}).invoke({"input":f"{input}"}, {"metadata": {"run_id_in_metadata": str(self.run_id_in_metadata)}})
  File "/usr/local/lib/python3.10/dist-packages/langchain/schema/runnable/base.py", line 2316, in invoke
    return self.bound.invoke(
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 84, in invoke
    return self(
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 306, in __call__
    raise e
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 300, in __call__
    self._call(inputs, run_manager=run_manager)
  File "/usr/local/lib/python3.10/dist-packages/langchain_experimental/plan_and_execute/agent_executor.py", line 56, in _call
    response = self.executor.step(
  File "/usr/local/lib/python3.10/dist-packages/langchain_experimental/plan_and_execute/executors/base.py", line 37, in step
    response = self.chain.run(**inputs, callbacks=callbacks)
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 506, in run
    return self(kwargs, callbacks=callbacks, tags=tags, metadata=metadata)[
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 306, in __call__
    raise e
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 300, in __call__
    self._call(inputs, run_manager=run_manager)
  File "/usr/local/lib/python3.10/dist-packages/langchain/agents/agent.py", line 1141, in _call
    next_step_output = self._take_next_step(
  File "/usr/local/lib/python3.10/dist-packages/langchain/agents/agent.py", line 925, in _take_next_step
    intermediate_steps = self._prepare_intermediate_steps(intermediate_steps)
  File "/usr/local/lib/python3.10/dist-packages/langchain/agents/agent.py", line 1258, in _prepare_intermediate_steps
    return self.trim_intermediate_steps(intermediate_steps)
  File "/app/utils.py", line 84, in fancier_trim_intermediate_steps
    return [steps[-1]]
IndexError: list index out of range
lil-jr-dev[bot] commented 1 year ago

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.

lil-jr-dev[bot] commented 1 year ago

Error in handle_issue_opened: list index out of range Traceback

Traceback (most recent call last):
  File "/app/utils.py", line 69, in fancier_trim_intermediate_steps
    log = Log(message=f"trim_intermediate_steps",
NameError: name 'Log' is not defined

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/app/github_webhook_handlers.py", line 96, in handle_issue_opened
    result = bot.run(prompt)
  File "/app/ml4bio_agent.py", line 34, in run
    result = self.agent.with_config({"run_name": "ML4BIO Plan & Execute Agent"}).invoke({"input":f"{input}"}, {"metadata": {"run_id_in_metadata": str(self.run_id_in_metadata)}})
  File "/usr/local/lib/python3.10/dist-packages/langchain/schema/runnable/base.py", line 2316, in invoke
    return self.bound.invoke(
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 84, in invoke
    return self(
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 306, in __call__
    raise e
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 300, in __call__
    self._call(inputs, run_manager=run_manager)
  File "/usr/local/lib/python3.10/dist-packages/langchain_experimental/plan_and_execute/agent_executor.py", line 56, in _call
    response = self.executor.step(
  File "/usr/local/lib/python3.10/dist-packages/langchain_experimental/plan_and_execute/executors/base.py", line 37, in step
    response = self.chain.run(**inputs, callbacks=callbacks)
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 506, in run
    return self(kwargs, callbacks=callbacks, tags=tags, metadata=metadata)[
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 306, in __call__
    raise e
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 300, in __call__
    self._call(inputs, run_manager=run_manager)
  File "/usr/local/lib/python3.10/dist-packages/langchain/agents/agent.py", line 1141, in _call
    next_step_output = self._take_next_step(
  File "/usr/local/lib/python3.10/dist-packages/langchain/agents/agent.py", line 925, in _take_next_step
    intermediate_steps = self._prepare_intermediate_steps(intermediate_steps)
  File "/usr/local/lib/python3.10/dist-packages/langchain/agents/agent.py", line 1258, in _prepare_intermediate_steps
    return self.trim_intermediate_steps(intermediate_steps)
  File "/app/utils.py", line 84, in fancier_trim_intermediate_steps
    return [steps[-1]]
IndexError: list index out of range
lil-jr-dev[bot] commented 1 year ago

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.

lil-jr-dev[bot] commented 1 year ago

Error in handle_issue_opened: list index out of range Traceback

Traceback (most recent call last):
  File "/app/utils.py", line 69, in fancier_trim_intermediate_steps
    log = Log(message=f"trim_intermediate_steps",
NameError: name 'Log' is not defined

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/app/github_webhook_handlers.py", line 96, in handle_issue_opened
    result = bot.run(prompt)
  File "/app/ml4bio_agent.py", line 34, in run
    result = self.agent.with_config({"run_name": "ML4BIO Plan & Execute Agent"}).invoke({"input":f"{input}"}, {"metadata": {"run_id_in_metadata": str(self.run_id_in_metadata)}})
  File "/usr/local/lib/python3.10/dist-packages/langchain/schema/runnable/base.py", line 2316, in invoke
    return self.bound.invoke(
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 84, in invoke
    return self(
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 306, in __call__
    raise e
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 300, in __call__
    self._call(inputs, run_manager=run_manager)
  File "/usr/local/lib/python3.10/dist-packages/langchain_experimental/plan_and_execute/agent_executor.py", line 56, in _call
    response = self.executor.step(
  File "/usr/local/lib/python3.10/dist-packages/langchain_experimental/plan_and_execute/executors/base.py", line 37, in step
    response = self.chain.run(**inputs, callbacks=callbacks)
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 506, in run
    return self(kwargs, callbacks=callbacks, tags=tags, metadata=metadata)[
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 306, in __call__
    raise e
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 300, in __call__
    self._call(inputs, run_manager=run_manager)
  File "/usr/local/lib/python3.10/dist-packages/langchain/agents/agent.py", line 1141, in _call
    next_step_output = self._take_next_step(
  File "/usr/local/lib/python3.10/dist-packages/langchain/agents/agent.py", line 925, in _take_next_step
    intermediate_steps = self._prepare_intermediate_steps(intermediate_steps)
  File "/usr/local/lib/python3.10/dist-packages/langchain/agents/agent.py", line 1258, in _prepare_intermediate_steps
    return self.trim_intermediate_steps(intermediate_steps)
  File "/app/utils.py", line 84, in fancier_trim_intermediate_steps
    return [steps[-1]]
IndexError: list index out of range
lil-jr-dev[bot] commented 1 year ago

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.

lil-jr-dev[bot] commented 1 year ago

Error in handle_issue_opened: list index out of range Traceback

Traceback (most recent call last):
  File "/app/utils.py", line 69, in fancier_trim_intermediate_steps
    log = Log(message=f"trim_intermediate_steps",
NameError: name 'Log' is not defined

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/app/github_webhook_handlers.py", line 96, in handle_issue_opened
    result = bot.run(prompt)
  File "/app/ml4bio_agent.py", line 34, in run
    result = self.agent.with_config({"run_name": "ML4BIO Plan & Execute Agent"}).invoke({"input":f"{input}"}, {"metadata": {"run_id_in_metadata": str(self.run_id_in_metadata)}})
  File "/usr/local/lib/python3.10/dist-packages/langchain/schema/runnable/base.py", line 2316, in invoke
    return self.bound.invoke(
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 84, in invoke
    return self(
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 306, in __call__
    raise e
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 300, in __call__
    self._call(inputs, run_manager=run_manager)
  File "/usr/local/lib/python3.10/dist-packages/langchain_experimental/plan_and_execute/agent_executor.py", line 56, in _call
    response = self.executor.step(
  File "/usr/local/lib/python3.10/dist-packages/langchain_experimental/plan_and_execute/executors/base.py", line 37, in step
    response = self.chain.run(**inputs, callbacks=callbacks)
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 506, in run
    return self(kwargs, callbacks=callbacks, tags=tags, metadata=metadata)[
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 306, in __call__
    raise e
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 300, in __call__
    self._call(inputs, run_manager=run_manager)
  File "/usr/local/lib/python3.10/dist-packages/langchain/agents/agent.py", line 1141, in _call
    next_step_output = self._take_next_step(
  File "/usr/local/lib/python3.10/dist-packages/langchain/agents/agent.py", line 925, in _take_next_step
    intermediate_steps = self._prepare_intermediate_steps(intermediate_steps)
  File "/usr/local/lib/python3.10/dist-packages/langchain/agents/agent.py", line 1258, in _prepare_intermediate_steps
    return self.trim_intermediate_steps(intermediate_steps)
  File "/app/utils.py", line 84, in fancier_trim_intermediate_steps
    return [steps[-1]]
IndexError: list index out of range
lil-jr-dev[bot] commented 1 year ago

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.

lil-jr-dev[bot] commented 1 year ago

Error in handle_issue_opened: list index out of range Traceback

Traceback (most recent call last):
  File "/app/utils.py", line 69, in fancier_trim_intermediate_steps
    log = Log(message=f"trim_intermediate_steps",
NameError: name 'Log' is not defined

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/app/github_webhook_handlers.py", line 96, in handle_issue_opened
    result = bot.run(prompt)
  File "/app/ml4bio_agent.py", line 34, in run
    result = self.agent.with_config({"run_name": "ML4BIO Plan & Execute Agent"}).invoke({"input":f"{input}"}, {"metadata": {"run_id_in_metadata": str(self.run_id_in_metadata)}})
  File "/usr/local/lib/python3.10/dist-packages/langchain/schema/runnable/base.py", line 2316, in invoke
    return self.bound.invoke(
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 84, in invoke
    return self(
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 306, in __call__
    raise e
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 300, in __call__
    self._call(inputs, run_manager=run_manager)
  File "/usr/local/lib/python3.10/dist-packages/langchain_experimental/plan_and_execute/agent_executor.py", line 56, in _call
    response = self.executor.step(
  File "/usr/local/lib/python3.10/dist-packages/langchain_experimental/plan_and_execute/executors/base.py", line 37, in step
    response = self.chain.run(**inputs, callbacks=callbacks)
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 506, in run
    return self(kwargs, callbacks=callbacks, tags=tags, metadata=metadata)[
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 306, in __call__
    raise e
  File "/usr/local/lib/python3.10/dist-packages/langchain/chains/base.py", line 300, in __call__
    self._call(inputs, run_manager=run_manager)
  File "/usr/local/lib/python3.10/dist-packages/langchain/agents/agent.py", line 1141, in _call
    next_step_output = self._take_next_step(
  File "/usr/local/lib/python3.10/dist-packages/langchain/agents/agent.py", line 925, in _take_next_step
    intermediate_steps = self._prepare_intermediate_steps(intermediate_steps)
  File "/usr/local/lib/python3.10/dist-packages/langchain/agents/agent.py", line 1258, in _prepare_intermediate_steps
    return self.trim_intermediate_steps(intermediate_steps)
  File "/app/utils.py", line 84, in fancier_trim_intermediate_steps
    return [steps[-1]]
IndexError: list index out of range
lil-jr-dev[bot] commented 1 year ago

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.

lil-jr-dev[bot] commented 1 year ago

👉 Follow the bot's progress in real time on LangSmith.

lil-jr-dev[bot] commented 1 year ago

Error in handle_issue_opened: 'NoneType' object is not subscriptable Traceback

Traceback (most recent call last):
  File "/app/github_webhook_handlers.py", line 107, in handle_issue_opened
    ray.get(post_comment.remote(issue_or_pr=issue, text=str(result['output']), time_delay_s=0))
TypeError: 'NoneType' object is not subscriptable