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workflowhub-eu / galaxy2cwl

Standalone version tool to get cwl descriptions (initially an abstract cwl interface) of galaxy workflows and Galaxy workflows executions.
BSD 3-Clause "New" or "Revised" License
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Error while running galaxy2cwl. #4

Open ambarishK opened 4 years ago

ambarishK commented 4 years ago

I am getting an error running the galaxy2cwl.py

  File "/usr/lib/python3.5/json/__init__.py", line 312, in loads
    s.__class__.__name__))
TypeError: the JSON object must be str, not 'bytes'

Please troubleshoot it.

ambarishK commented 4 years ago

Hi Ignacio Eguinoa.

I think this is due to encoding issue. I am using ubuntu 16.04 and python 3.6.

ieguinoa commented 4 years ago

Hi!

I'm trying to replicate the error, could you tell me which input file you've used for the run?

ambarishK commented 4 years ago

I am using Haplotypecaller.ga.

ieguinoa commented 4 years ago

problem is in the python lib (actually in the built-in json lib). For python 3.5 the json loader expects a string while in Python 3.6 this should be a byte object. can you test with python 3.6 ? I will try to generalize the loading anyway.

ieguinoa commented 4 years ago

I pushed a fix for it, should work with 3.5 too now.

ambarishK commented 4 years ago

Let me check.

Error persists even with Python 3.6

ieguinoa commented 4 years ago

for the error you showed it seems that you are using python 3.5. Have you updated galaxy2cwl with the new changes? are you installing from pip or from the repo?

ambarishK commented 4 years ago

Got fixed.

I have acknowledged your name in workflow group proceedings and will keep working it as a project integrated with other projects like cloud based Bioinformatics to make it a matured publication.

What is other way of communication with you? Do you remain active ( regular checking issues ) over github?

Converting other workflows to CWL tools.

ambarishK commented 4 years ago

Hi I have added your name over here - https://github.com/heuermh/bh20-workflows-bhxiv/blob/master/paper.md

ieguinoa commented 4 years ago

Hi,

thanks for the acknowledgement, I will keep an eye on that work too, looks interesting. About this project (galaxy2cwl) in particular, you can always ask about it in the issues. For any other things I'm available through gitter.

Cheers, Ignacio