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algbio / ggcat

Compacted and colored de Bruijn graph construction and querying
MIT License
72 stars 10 forks source link

installation not working #1

Closed marade closed 1 year ago

marade commented 1 year ago

[22:18:22 ~/ggcat]$ curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh ... [22:18:48 ~/ggcat]$ source "$HOME/.cargo/env" [22:18:51 ~/ggcat]$ which cargo /home/ubuntu/.cargo/bin/cargo [22:19:27 ~/ggcat]$ ls -la /home/ubuntu/.cargo/bin/ total 200936 drwxrwxr-x 2 ubuntu ubuntu 4096 Oct 25 22:12 . drwxrwxr-x 3 ubuntu ubuntu 4096 Oct 25 22:13 .. -rwxr-xr-x 13 ubuntu ubuntu 15825920 Oct 25 22:11 cargo -rwxr-xr-x 13 ubuntu ubuntu 15825920 Oct 25 22:11 cargo-clippy -rwxr-xr-x 13 ubuntu ubuntu 15825920 Oct 25 22:11 cargo-fmt -rwxr-xr-x 13 ubuntu ubuntu 15825920 Oct 25 22:11 cargo-miri -rwxr-xr-x 13 ubuntu ubuntu 15825920 Oct 25 22:11 clippy-driver -rwxr-xr-x 13 ubuntu ubuntu 15825920 Oct 25 22:11 rls -rwxr-xr-x 13 ubuntu ubuntu 15825920 Oct 25 22:11 rust-gdb -rwxr-xr-x 13 ubuntu ubuntu 15825920 Oct 25 22:11 rust-gdbgui -rwxr-xr-x 13 ubuntu ubuntu 15825920 Oct 25 22:11 rust-lldb -rwxr-xr-x 13 ubuntu ubuntu 15825920 Oct 25 22:11 rustc -rwxr-xr-x 13 ubuntu ubuntu 15825920 Oct 25 22:11 rustdoc -rwxr-xr-x 13 ubuntu ubuntu 15825920 Oct 25 22:11 rustfmt -rwxr-xr-x 13 ubuntu ubuntu 15825920 Oct 25 22:11 rustup [22:19:31 ~/ggcat]$ cargo install --path . error: found a virtual manifest at /home/ubuntu/ggcat/Cargo.toml instead of a package manifest

Additionally (not an issue) for the paper, consider comparing to BlastFrost instead of Bifrost for the queries:

https://github.com/nluhmann/BlastFrost

Thanks for your work on this interesting tool!

Guilucand commented 1 year ago

Hi, I switched to a workspace project type and forgot to update the install instructions. The updated working command is:

cargo install --path cmdline/

I've updated the README file with the correct command.

Thanks for the suggestion, we'll check BlastFrost and update the benchmarks.

marade commented 1 year ago

Great, this appears to work. Looking forward to testing this tool.