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AndriiPovsten / Snakemake-backend-for-RECAST

Snakemake implementation for RECAST
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Reana client #16

Closed AndriiPovsten closed 1 year ago

AndriiPovsten commented 1 year ago

Dear @matthewfeickert could you please check the latest commit to this PR? I reproduced the blog post Support for running Snakemake workflows and it seems like working with our reana-environment.yml file. But for Hello_word example after entering this command reana-client run -f reana-snakemake.yaml the error is this:

File "/Users/povsten/opt/anaconda3/envs/Snakemake-reana-helloworld-example/lib/python3.11/site-packages/ratelimiter.py", line 127, in RateLimiter
    __aexit__ = asyncio.coroutine(__exit__)
                ^^^^^^^^^^^^^^^^^
AttributeError: module 'asyncio' has no attribute 'coroutine'
==> ERROR: Cannot create workflow : 
Snakemake specification is invalid.

But the .snakemake workflow was created but with empty output. I guess that I missed some dependencies. Do you know what could cause such an error?

AndriiPovsten commented 1 year ago

Dear @matthewfeickert, I asked in the Mattermost channel for a possible solution and the error was that it was currently impossible to submit a Snakemake workflow from Python 3.11, so I switched to Python 3.10 and now the Snakemake workflow seems to run successfully.

AndriiPovsten commented 1 year ago

Dear @matthewfeickert, my latest commit workflow seems to work with REANA. I know it's a much lighter version, but I think I get the principle of how workflows work in REANA. Could you please review the changes? Or give more complex RECAST examples?