When running generate_submission.sh for predict_modality, can't find main.nf

[dburkhardt]

When running the generate_submission.sh script at https://github.com/openproblems-bio/neurips2021_multimodal_viash/blob/main/src/predict_modality/starter_kit/starter_kit_r/generate_submission.sh from within the starter_kit_r directory

I get the following error:

❯ ./generate_submission.sh

######################################################################
##              Build docker executable and container               ##
######################################################################
./generate_submission.sh: line 14: viash: command not found
❯ viash
zsh: command not found: viash
❯ export PATH=~/repos/neurips2021_multimodal_viash/bin:$PATH
❯ ./generate_submission.sh

######################################################################
##              Build docker executable and container               ##
######################################################################
[notice] Running 'docker build -t method:dev /tmp/viashsetupdocker-method-F0pt9C'

######################################################################
##                      Build nextflow module                       ##
######################################################################
> input_mod1 in method is set to be required.
> --input_mod1 <...> has to be specified when running this module standalone.
> input_mod2 in method is set to be required.
> --input_mod2 <...> has to be specified when running this module standalone.
> output in method is set to be required.
> --output <...> has to be specified when running this module standalone.

######################################################################
##            Generating submission files using nextflow            ##
######################################################################
N E X T F L O W  ~  version 21.04.1
Pulling openproblems-bio/neurips2021_multimodal_viash ...
 downloaded from https://github.com/openproblems-bio/neurips2021_multimodal_viash.git
Missing project main script: /Users/dburkhardt/.nextflow/assets/openproblems-bio/neurips2021_multimodal_viash/src/predict_modality/workflows/generate_submission/main.nf

When I look in that directory, I see the following:

> ls /Users/dburkhardt/.nextflow/assets/openproblems-bio/neurips2021_multimodal_viash/src/predict_modality/workflows/
generate_task1_submission       prepare_task1_datasets          run_task1_benchmark             run_task1_standalone_evaluation```

[dburkhardt]

Okay it looks like the issue is it's pulling from the most recent release, but that's out of date

[rcannood]

Ah, yes. I need to create a new release with all of the latest changes. You can use -r main_build for now.

[rcannood]

I committed some uncommitted changes that I had sitting around prior to our meeting yesterday. It should work now :)