Ming 'Tommy' TangJul 6, 2025
1/ Bioinformatics sounds exciting—until you spend 6 hours just trying to install a tool.
Even after 12 years for me, tool setup still sucks.
Especially on a new Mac with an M3 chip.
Let’s talk about it. 🧵
Show threadMing 'Tommy' TangJul 6, 2025
2/
I was building a tutorial to replicate Figure 1 of a paper:
https://github.com/crazyhottommy/reproduce_genomics_paper_figures
But before I could even look at the data…
I was stuck trying to install the tools.
GitHub - crazyhottommy/reproduce_genomics_paper_figures: step by step tutorial in the website

step by step tutorial in the website. Contribute to crazyhottommy/reproduce_genomics_paper_figures development by creating an account on GitHub.

GitHub
Show threadMing 'Tommy' TangJul 6, 2025
3/
I’m using a MacBook Pro with the new M3 chip.
That’s where the trouble starts.
Many bioinformatics tools aren’t optimized for Apple Silicon.
Even with Conda, you’ll hit brick walls.
Show threadMing 'Tommy' TangJul 6, 2025
4/
Example 1:
I needed fastq-dl to download FASTQ files from GEO.
But… nope.
fastq-dl depends on sra-tools, and sra-tools doesn’t support macOS M3.
Dead end.
Show threadMing 'Tommy' TangJul 6, 2025
5/
Example 2:
Tried installing Bowtie2 for read alignment.
Error: libcxx >= 16 is missing
Now I’m deep in dependency hell before I’ve written a single line of analysis code.
Show threadMing 'Tommy' TangJul 6, 2025
6/
Beginner or not—this stuff burns time.
You lose a whole day to install errors.
Frustration sets in.
You start questioning if you belong in this field.
Show threadMing 'Tommy' TangJul 6, 2025
7/
Sure, Docker or Mamba can help.
But Docker itself isn’t always intuitive.
Now you're installing something to help you install something else.
Show threadMing 'Tommy' TangJul 6, 2025
8/
This is the first true test in bioinformatics:
“Can I install the tool?”
Not “Is it accurate?”
Not “Is it published?”
If I can’t run it, I can’t use it. Period.
Show threadMing 'Tommy' Tang
9/
My rule now:
If a tool doesn’t install cleanly in 30 minutes, I ditch it.
Not because I’m lazy—
Because I respect my time. (I do have to fight for hours if the tool is the only option...)
Jul 6, 2025 at 1:15pmWeb
Show threadMing 'Tommy' TangJul 6, 2025
10/
What can make this better?
– Clear install instructions
– Pre-built containers (Docker/Singularity)
– Support for M1/M2/M3 chips
– Active community troubleshooting
– Smarter packaging (e.g. Bioconda, Homebrew, precompiled binaries)
Show threadMing 'Tommy' TangJul 6, 2025
11/
If you’re building bioinformatics tools:
Treat installation as part of UX.
Because if it’s painful to install, it won’t matter how brilliant your algorithm is.
Show threadMing 'Tommy' TangJul 6, 2025
12/
Tool installation shouldn’t be a rite of passage.
We need frictionless starts—especially for the next generation of scientists.
Show threadMing 'Tommy' TangJul 6, 2025
13/
So next time someone says “bioinformatics is just running a few tools,”
tell them:
Yeah, once you manage to install them.
Let’s make it better.
Show threadMing 'Tommy' TangJul 6, 2025

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