[build] --cpus isn't passed to thru when using --exec

[corneliusroemer]

Current Behavior

Invoking nextstrain build --docker or (--aws-batch) does not pass --cores option to snakemake causing error:

Error: you need to specify the maximum number of CPU cores to be used at the same time. If you want to use N cores, say --cores N or -cN. For all cores on your system (be sure that this is appropriate) use --cores all. For no parallelization use --cores 1 or -c1. <_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'>

Expected behavior

Nextstrain cli passes that argument to snakemake so that the error doesn't happen

How to reproduce

Steps to reproduce the current behavior:

1. gh repo clone nextstrain/rsv
2. cd rsv
3. Run

nextstrain build \
    --docker \
    --detach \
    --no-download \
    --cpus 5 \ 
--exec env \
    . \
      snakemake \
        --configfiles config/configfile.yaml  \
        --printshellcmds

Environment

• Operating system: macOS 13.3.1 on M1
• shell: zsh
• version: nextstrain.cli 6.2.1

Additional context

This error could be behind most of the snakemake workflow errors we've been getting since the snakemake upgrade in docker.

[corneliusroemer]

The issue appears iff the cli build command contains the snakemake magic word.

This alternative way, without --exec and without env and snakemake works:

nextstrain build \
    --docker \
    --detach \
    --no-download \
    --cpus 5 \
    . \
    --configfiles config/configfile.yaml  \
        --printshellcmds

I'm confused about the --exec option, it is not documented in nextstrain build --help

I see! It's in --help-all under development options
--exec <prog> Program to run inside the runtime (default: snakemake)

So the way we invoke things in the actions is not how we usually document how to run nextstrain builds (without --exec, using the default snakemake.

[tsibley]

Ah, yes, that'd be an issue. Nextstrain CLI only passes thru --cpus as Snakemake's --cores when the program its running (--exec) is snakemake:

cli/nextstrain/cli/command/build.py

Lines 141 to 144 in 7b23f56

	# Automatically pass thru appropriate resource options to Snakemake to
	# avoid the user having to repeat themselves (once for us, once for
	# snakemake).
	if opts.exec == "snakemake":

[tsibley]

In those GitHub Actions workflows which launch our pathogen workflows, we use env purely to keep the rest of the command (envdir … snakemake …) together, IIRC. We could drop --exec env, but then we'd have to replace it with --exec envdir in order to use the env dir we create.

Since 2018, I've wanted to integrate env var management for nextstrain build via first-class env dir support (so we don't have to do this hacky thing), but it's never floated to the top of the list. This is maybe a good reason to prioritize it (but there's also so many other things to prioritize).

[tsibley]

(Summary notes on env var management for Nextstrain CLI and our pathogen workflows.)

[jameshadfield]

Since 2018, I've wanted to integrate env var management for nextstrain build via first-class env dir support (so we don't have to do this hacky thing)

Beyond the immediate PRs which will (probably?) close this issue, I think this would be a great thing to prioritise. I remember having to dive into the CLI code to write some of these actions, doubly complicated by my lack of familiarity with envdir (summarised in this slack thread). Doing this would have two wins: it removes the need for --exec and thus makes the GitHub actions syntax for nextstrain build more familiar (helps with debugging, readablitiy and lack of gotchas); secondly we become used to explicitly passing through env variables rather than having to know about this list.