fix shell init, add sra-tools

[helmingstay]

• On debian, ~/.local/bin isn't in path by default
  • update to shell hook fixes this.
• nvd_cli_guide.md provides an example for SRA accessions. In this example, FETCH_FASTQ fails because sra-tools (prefetch and fasterq-dump) are not included in the pipeline image.
  • update pyproject.toml and pixi.lock to include sra-tools

Consider bumping version to 3.0.1?

[nrminor]

Hi @helmingstay -

Apologies for the very long delay in our getting back to you. Thanks for catching these issues.

The missing dependency for SRA download happens to have already been released in the v3.0.1 release candidate we just merged. We also have other upcoming release candidates, though, e.g. #29 and #32, where we could put the shell fix.

Before I think about pulling out and rebasing your commit efac02a, is there any way we could make $PATH availability more cross-platform without noodling with users' RC files? I agree that that would work as a solution, but it's a pet peeve of mine that so many tools want to mutate my RC files, which sooner or later can cause confusing $PATH availability issues.

Let me know if that doesn't make sense or if you have any ideas.

Thanks for taking the time!

[helmingstay]

Makes sense. I found that the installer provided helpful feedback throughout the process, so my preference here would be A) check and B) ask. Simply echoing something like, "Detected zsh but nvd not in path. Paste this line to fix:
cat PATH=$PATH:... >> ~/.zshrc
"
Presents the user with the issue and the solution, providing sufficient information to modify the solution if needed and just accept it if not.

[nrminor]

I like that idea a lot. Would you like to implement that in this or another PR, or shall I? Either works for me.

Thanks again!

[helmingstay]

I'm happy leaving it to you! -Christian

…

On Fri, Jul 10, 2026, 19:02 Nick Minor ***@***.***> wrote: *nrminor* left a comment (dholab/nvd#27) <#27 (comment)> I like that idea a lot. Would you like to implement that in this or another PR, or shall I? Either works for me. Thanks again! — Reply to this email directly, view it on GitHub <#27?email_source=notifications&email_token=AAEXA5KCI4J2O6EHRTCFUA35EFYWVA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTIOJUGAZDAOBTHEZ2M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLDGN5XXIZLSL5RWY2LDNM#issuecomment-4940208393>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAEXA5OM7NTRWYXSO7XFJD35EFYWVAVCNFSNUABFKJSXA33TNF2G64TZHM4DKNBYG44DIMZWHNEXG43VMU5TINRSG43DIOBUGIZKC5QC> . You are receiving this because you were mentioned.Message ID: ***@***.***>