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snakemake / snakeface

The snakemake interface, currently works like a notebook (under development)
https://snakeface.readthedocs.io/
Mozilla Public License 2.0
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Instructions to run a pipeline via snakeface #19

Closed fgypas closed 3 years ago

fgypas commented 3 years ago

Hi @vsoch

Can you please tell me how can I run a simple pipeline via snakeface?

When I run something like the following:

snakeface \
--port 5432 \
https://github.com/panoptes-organization/snakemake_example_workflow \
this_is_a_test \
notebook

I get a message:

You don't have any Snakemake workflows. Why don't you create one?

And when I click on create one I get a message:

No Snakefiles were found in any path under /Users/gypafoiv/Desktop/snakeface. You must have one to create a workflow.

What am I doing wrong?

Thank you in advance

vsoch commented 3 years ago

I'm not sure why you are adding a GitHub url to the command (it could be a use case but is not developed yet). You would need to have a Snakefile in the root or somewhere in a subfolder where you run Snakeface. So you can take this verbatim:

No Snakefiles were found in any path under /Users/gypafoiv/Desktop/snakeface. You must have one to create a workflow.

vsoch commented 3 years ago

Where did you read to formulate that command? And what is this_is_a_test and notebook?

vsoch commented 3 years ago

Instead of having it work like an ipython notebook to look for files already existing, we could have it work to provide a url with a workflow and then the workflow is cloned somewhere and deployed and run. But I suspect most users will want to customize things first.

fgypas commented 3 years ago

Ah, ok sorry. I relied on the following:

usage: snakeface [-h] [--version] [--noreload] [--verbosity {0,1,2,3}]
                 [--workdir [WORKDIR]] [--auth {token}] [--port PORT]
                 [--quiet] [--verbose] [--log-disable-color]
                 [--log-use-threads] [--force]
                 [repo] [dest] {notebook} ...

and I assumed that repo is a github repo and dest is the destination where the repo is cloned, and notebook is just the notebook mode.

I will try again with a locally cloned pipeline and ping you again.

vsoch commented 3 years ago

The little tutorial provided is here: https://snakeface.readthedocs.io/en/latest/getting_started/example_workflow.html.

I think repo and dest are actually erroneously there because I probably copied the functionality from the snakedeploy script! I'll open a PR to remove them.

fgypas commented 3 years ago

Great. Thanks a lot! I am following this now.