cli

cli copied to clipboard

`Your request was too big` error on stock RSV repo build via aws-batch

7

### Current Behavior When trying to run the nextstrain/rsv workflow using `nextstrain build --aws-batch ...` I get an error: `botocore.exceptions.ClientError: An error occurred (MaxMessageLengthExceeded) when calling the PutObject operation: Your...

corneliusroemer

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

5

### 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...

corneliusroemer

### Context When updating the managed conda env, I noticed that it installed an old version of nextstrain cli. We should probably auto-trigger conda-base rebuilds on release of new cli.

corneliusroemer

Add command to self-upgrade

3

### Context When updating `nextstrain` runtimes, I was told that a new cli version is available and that I should update using: ``` mamba install -p /opt/homebrew/Caskroom/miniforge/base/envs/nextstrain nextstrain-cli==6.2.1 ``` That...

corneliusroemer

Confusing log message "runtime updated" when nothing was changed

3

### Current Behavior The logs for `nextstrain update conda` report "Runtime updated!" in green, despite no update having happened. ### Expected behavior "Runtime updated!" only shows when an update has...

corneliusroemer

ENH: Print docker image used at beginning of aws-batch jobs

2

I was trying to see why a bug happened in a recent monkeypox CI run. I couldn't reproduce locally using the latest docker-base image. I couldn't figure out which docker...

corneliusroemer

[batch] exclude directories for upload

9

### Context Deploying a build to AWS-batch currently zips up (almost) the entire current directory and uploads this to S3. [Certain assets are not uploaded, e.g. `.git/`, but these are...

jameshadfield

### Current Behavior When users run the `nextstrain build` command from Windows with Docker and provide an argument to Snakemake that references a local path using backslashes (e.g., `nextstrain build...

huddlej

[setup] Docker runtime support

1

With the new `nextstrain setup` command that will soon land as part of #218, the framework is in place for runner modules to automatically set up their runtime. It appears...

tsibley

### Current Behavior The CLI's nextstrain.org remote for `nextstrain remote {ls,download,delete}` treats paths as case-sensitive: https://github.com/nextstrain/cli/blob/cf0f3486ec785b6f9f988696d6c30ede363a3494/nextstrain/cli/remote/nextstrain_dot_org.py#L396-L400 In general, they are so this is fine, but the names of Nextstrain Groups...

tsibley