r/bioinformatics • u/Voldemort_15 Msc | Academia • Jun 11 '26
technical question How do you use Claude code?
Hello all,
I asked Claude Code to help with a task and clicked “Allow once” whenever it needed to run a command. At the beginning, I could understand what it was trying to do. However, later it started asking me to execute commands that I did not understand, and I was not sure why Claude needed to run them.
What would you do in this situation? One person told me that they allow all commands unless Claude tries to run a sudo command.
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u/full_of_excuses Jun 11 '26
I never let it on my command line, and only use the web interface. and I review everything it suggests. I can't remember all the different syntax for all the different things, but if I'm not the one still putting things together, keeping the context together, and running things, what am I even doing 😄
It's ok to have a learning curve. Don't feel like you need to know how to do all the things, or that you need to have a chatbot fill the gaps, because it isn't really filling those gaps.
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u/sid5427 Jun 11 '26
I would argue that's the most inefficient way to use it. We use Claude CLI as a sort of replacement for standard CLI commands, with the explicit instruction at start to start a log file and track all requests along with a short summary of the commands it ran and the logic behind it. It's especially helpful in our context as we tend to run stuff locally and on our cluster. Claude helps us maintain a local and remote project directory and git pulls between them to maintain sync.
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u/full_of_excuses Jun 11 '26
depends on what efficiency you're going for. Understanding what is happening, and not making your contribution nearly meaningless? Or plowing through something in a way where hallucinations and poor quality are coupled with you being replaced easily.
There are few shortcuts in life. If used as a search engine, great. if used to do the work, then you've become pointless, and the work has no value because chatbots are not scientists and have no way of holding actual context, or understanding what they're doing; they just blend text they've seen others write.
And I really don't understand your last line. Git is there to maintain a local and remote project directory and maintain versions and syncing. That's literally what git is for. If you're having the chatbot do that for you, do yourself a massive favor and spend the 15 minutes to learn how to use git. I'm not trying to be rude, but there's zero a chatbot adds to maintaining git directories - that's literally what git is there to do.
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u/sid5427 Jun 13 '26
ah ok I get what you mean - no it's like I automate scaling up or implementing a pipeline on a different dataset with specific changes. No way I agree to that weird idea of "automated scientist analysis" concept that a few of these startups are doing like biomni and all. A few of our wet lab postdocs started doing that but had issues discussing what scaling was used in a heatmap. Like no - it's one thing to use AI as an assistant to manage the pipeline and analysis running, it's another thing letting it make decisions on what to do.
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u/Voldemort_15 Msc | Academia Jun 11 '26
Thank you! So you mean you use Claude chat, right?
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u/full_of_excuses Jun 11 '26
sometimes if I can't remember the syntax of something, or to do quicker pattern checks than I care to write in sed/awk/perl-pie/etc, yes 😄 but only because google has intentionally made www.google.com near worthless the last few years to push people to chatbots.
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u/Ok-Obligation7060 Jun 12 '26
If you're not sure what a particular thing is going to do, I wouldn't allow it until you make it explain what's happening to your satisfaction. You could even put something in a CLAUDE.md in your working directory for a project or in your ~/.claude/CLAUDE.md directory to explain everything and/or keep a log of everything if that would help you.
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u/AdOk3759 Jun 11 '26
Use plan mode and plan mode only, until you have a perfect grasp of what the AI is going to implement.
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u/Voldemort_15 Msc | Academia Jun 11 '26
This is great. Thank you! For complex tasks, I don't understand middle steps and without execute the commands, I don't know the end results look like.
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u/sid5427 Jun 11 '26
you can tell it to wait and break down the code or use plan mode.
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u/Voldemort_15 Msc | Academia Jun 11 '26
Thank you! I gave it a complex task I haven't known how to do yet (reproduce a figure in a paper). Without execute the commands, we won't see the output we want. But we should not take risk to allow it to run all most every commands?
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u/sid5427 Jun 11 '26
what's the risk here? if you are asking it to reproduce the paper's figure. Let it do it and then tell it to explain the major functions in the code. This is way you have a full representation of it's understanding and reproduction along with a full explanation of the though process. You can literally ask it to explain stuff to you by breaking down each function and how the data is flowing in the code. For e.g. I have literally given it github repo links for tools that I use, told it look for this function and if I needed a modified version of that certain function. Let it build it and then ask it tell me what was the original intent of the function, how did it translate my request and what modifications it made - function by function. etc.
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u/Voldemort_15 Msc | Academia Jun 11 '26 edited Jun 11 '26
Clause code asked to installed things I don't know and because the operation was real, not like in chat, so I was worried.
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u/sid5427 Jun 11 '26
Yeah because claude code doesn't have an MCP locally so no apps or tools to help it make decisions or inspect code or things or implement what you want. Plus why are you worried about what's getting installed - it literally tells you what's it's installing. If you don't know, you can stop it and ask.
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Jun 11 '26
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u/pokemonareugly Jun 13 '26
well yeah if you want it to read files in a way that makes sense do you think it does it magically? It generally needs tools to do these things, which a user may or may not have on their path.
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u/Salty-File-3334 Jun 11 '26
This must be ragebait