Error while running galaxy2cwl.

[ambarishK]

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]

Hi Ignacio Eguinoa.

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

[ieguinoa]

Hi!

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

[ambarishK]

I am using Haplotypecaller.ga.

[ieguinoa]

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]

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

[ambarishK]

Let me check.

Error persists even with Python 3.6

[ieguinoa]

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]

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]

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

[ieguinoa]

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