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Troubleshooting

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Edward O'Donnell edited this page Oct 11, 2021 · 3 revisions

Common problems and their solutions

  1. When running create_meta.py, the bioformats package complains about missing OMEXML, make sure these packages are at these versions as of July 2021:
    1. Python 3.6.9 on Ubuntu 18.04
      1. bioformats==0.1.15
      2. python-bioformats==4.0.3
      3. numpy==1.19.3
      4. python-javabridge==4.0.2
    2. Python 3.8.10 on Ubuntu 20.04
      1. bioformats==0.1.15
      2. python-bioformats==4.0.5
      3. numpy==1.21.0
      4. python-javabridge==4.0.3
      5. igneous-pipeline==0.8.2 (as of Oct 2021)
  2. NOTE! numpy==1.21.0 does not work with the earlier versions of igneous-pipeline. (below 0.1.0)

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