Error compiling development instance about nextclade HOT 7 CLOSED

@ArtPoon It's not a compilation error, but a runtime error from Nextclade.

The comment in the guide suggests to retrieve a dataset first:

This is what Nextclade software requires as inputs and cargo run just compiles and then runs Nextclade with the specified flags.

It is mentioned only briefly in dev docs, because when I wrote it, I assumed Nextclade devs are already familiar with Nextclade from user's standpoint. But we've actually already had a similar situation where this assumption turned out to be incorrect. So perhaps we need to add a command for downloading a dataset to the dev docs. But it's a nuanced topic and as a dev you probably want to have multiple datasets. or even all of them from https://github.com/nextstrain/nextclade_data, perhaps some tweaked/custom datasets etc. We need to decide what is most appropriate for the dev guide.

from nextclade.

Ok find command located binary in target/release. Just did a brute force copy of binary to /usr/local/bin.

from nextclade.

Adding a nextclade dataset command before the run step to the dev docs should fix this issue in the future. See #1145

@ArtPoon I think this is the step that errored, right?

cargo run --bin=nextclade -- run \
  data_dev/sequences.fasta \
  --input-dataset=data_dev/ \
  --output-fasta='out/nextclade.aligned.fasta' \
  --output-tsv='out/nextclade.tsv' \
  --output-tree='out/nextclade.tree.json' \
  --in-order \
  --include-reference
    Finished dev [unoptimized + debuginfo] target(s) in 0.25s
     Running `target/debug/nextclade run data_dev/sequences.fasta --input-dataset=data_dev/ --output-fasta=out/nextclade.aligned.fasta --output-tsv=out/nextclade.tsv --output-tree=out/nextclade.tree.json --in-order --include-reference`

from nextclade.

Yes that did the trick. Sorry for my noob question!

(venv) art@Kestrel:~/git/nextclade$ cargo run --bin=nextclade -- dataset get --name=sars-cov-2 --output-dir=data_dev
    Finished dev [unoptimized + debuginfo] target(s) in 0.41s
     Running `target/debug/nextclade dataset get --name=sars-cov-2 --output-dir=data_dev`
(venv) art@Kestrel:~/git/nextclade$ cargo run --bin=nextclade -- run   data_dev/sequences.fasta   --input-dataset=data_dev/   --output-fasta='out/nextclade.aligned.fasta'   --output-tsv='out/nextclade.tsv'   --output-tree='out/nextclade.tree.json'   --in-order   --include-reference
    Finished dev [unoptimized + debuginfo] target(s) in 0.21s
     Running `target/debug/nextclade run data_dev/sequences.fasta --input-dataset=data_dev/ --output-fasta=out/nextclade.aligned.fasta --output-tsv=out/nextclade.tsv --output-tree=out/nextclade.tree.json --in-order --include-reference`
(venv) art@Kestrel:~/git/nextclade$ cargo build --release --bin=nextclade
   Compiling libc v0.2.126
...
   Compiling nextclade v2.13.1 (/home/art/git/nextclade/packages_rs/nextclade)
   Compiling nextclade-cli v2.13.1 (/home/art/git/nextclade/packages_rs/nextclade-cli)
    Finished release [optimized] target(s) in 3m 47s
(venv) art@Kestrel:~/git/nextclade$ ./target/release/nextclade run \
>   data_dev/sequences.fasta \
>   --input-dataset=data_dev/ \
>   --output-fasta='out/nextclade.aligned.fasta' \
>   --output-tsv='out/nextclade.tsv' \
>   --output-tree='out/nextclade.tree.json' \
>   --in-order \
>   --include-reference

However there is no nextclade binary.

from nextclade.

Sorry, this is of course not obvious to non-rustaceans! :)

from nextclade.

We should probably link to the Rust Book and Cargo Book in the docs.

https://doc.rust-lang.org/book/

https://doc.rust-lang.org/cargo/

And perhaps also docs for other important tech stack components: Typescript, Node.js, yarn, React, Recoil and Next.js

There's a lot of things to know before a complex app like this can be understood.

from nextclade.

Certainly linking this particular page would be helpful:
https://doc.rust-lang.org/book/ch01-03-hello-cargo.html

from nextclade.