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CAMI-challenge / OPAL

OPAL: Open-community Profiling Assessment tooL
https://cami-challenge.github.io/OPAL/
Apache License 2.0
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Error when running tsv2biom.py #24

Closed muslih14 closed 6 years ago

muslih14 commented 6 years ago

Thanks for the awesome script.

I've followed the installation and have been able to run OPAL but I'm having an issue with the tsv2biom.py script. When I run the example: python3 tsv2biom.py data/cranky_wozniak_13 -o output_dir/cranky_wozniak_13.biom I keep getting : "Input file could not be read" error

sjanssen2 commented 6 years ago

As an alternative, I suggest

  1. installing miniconda
  2. create an python3 conda environment
  3. install native "biom-format" and "h5py" conda packages to finally call biom convert --to-hdf5 -i input.tsv -o output.biom
muslih14 commented 6 years ago

My input file for biom convert is in the CAMI biobox format. Will the biom output using biom convert work with Opal?

fernandomeyer commented 6 years ago

Fixed. @muslih14 Thanks for reporting the error. The output of biom convert does not work with OPAL.

muslih14 commented 6 years ago

Thank you, fernando! I will give it a try right now. I hope you can indulge me this question : I'm looking to convert SuperFOCUS and FOCUS outputs to biom or the CAMI bioboxes format. Do you know of any tool that I could use?

fernandomeyer commented 6 years ago

@muslih14 There is a biobox (docker container) that automatically converts the output of FOCUS to the CAMI bioboxes format. See: https://github.com/CAMI-challenge/docker_profiling_tools/tree/master/focus

muslih14 commented 6 years ago

Thank you, Fernando!

On Thu., 12 Apr. 2018, 8:17 am fernandomeyer, notifications@github.com wrote:

@muslih14 https://github.com/muslih14 There is a biobox (docker container) that automatically converts the output of FOCUS to the CAMI bioboxes format. See: https://github.com/CAMI-challenge/docker_profiling_tools/tree/master/focus

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