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RobJY avatar RobJY commented on August 17, 2024

Hi @jmuhlich, I've got a few questions about the marker sheets:

  • is there a marker sheet for the tonsil data?
  • I'm looking at the marker sheet for the exemplar data. Are there other allowed columns besides the ones in this sheet?
    • Columns in that file are: channel_number, cycle_number, marker_name, Filter, excitation_wavelength, emission_wavelength
  • Which columns are required?

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RobJY avatar RobJY commented on August 17, 2024

Hmm, I get ilastik_pixelclassification to start, but it errors out with:

Command error:
  Unable to find image 'biocontainers/ilastik:1.4.0_cv1' locally
  1.4.0_cv1: Pulling from biocontainers/ilastik
  677076032cca: Pulling fs layer
  1caf95c15ee1: Pulling fs layer
  8c24ac808f6a: Pulling fs layer
  acf6bb56eb1c: Pulling fs layer
  acf6bb56eb1c: Waiting
  8c24ac808f6a: Verifying Checksum
  8c24ac808f6a: Download complete
  677076032cca: Verifying Checksum
  677076032cca: Download complete
  677076032cca: Pull complete
  acf6bb56eb1c: Verifying Checksum
  acf6bb56eb1c: Download complete
  1caf95c15ee1: Verifying Checksum
  1caf95c15ee1: Download complete
  1caf95c15ee1: Pull complete
  8c24ac808f6a: Pull complete
  acf6bb56eb1c: Pull complete
  Digest: sha256:1900d2ef1f53acbd4fa180f706cc2ea9d7fca25ff8e161201b97f2aa93fdd9e4
  Status: Downloaded newer image for biocontainers/ilastik:1.4.0_cv1
  Matplotlib created a temporary config/cache directory at /tmp/matplotlib-sdpzk4kf because the default path (/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
  Traceback (most recent call last):
    File "/opt/ilastik-1.4.0-Linux/bin/ilastik", line 10, in <module>
      sys.exit(main())
    File "/opt/ilastik-1.4.0-Linux/lib/python3.7/site-packages/ilastik_scripts/ilastik_startup.py", line 146, in main
      main()
    File "/opt/ilastik-1.4.0-Linux/lib/python3.7/site-packages/ilastik/__main__.py", line 30, in main
      hShell = app.main(parsed_args, workflow_cmdline_args)
    File "/opt/ilastik-1.4.0-Linux/lib/python3.7/site-packages/ilastik/app.py", line 134, in main
      _init_logging(parsed_args)  # Initialize logging before anything else
    File "/opt/ilastik-1.4.0-Linux/lib/python3.7/site-packages/ilastik/app.py", line 293, in _init_logging
      default_config.init(process_name, default_config.OutputMode.BOTH, logfile_path)
    File "/opt/ilastik-1.4.0-Linux/lib/python3.7/site-packages/ilastik/ilastik_logging/default_config.py", line 233, in init
      os.makedirs(os.path.dirname(DEFAULT_LOGFILE_PATH), exist_ok=True)
    File "/opt/ilastik-1.4.0-Linux/lib/python3.7/os.py", line 213, in makedirs
      makedirs(head, exist_ok=exist_ok)
    File "/opt/ilastik-1.4.0-Linux/lib/python3.7/os.py", line 213, in makedirs
      makedirs(head, exist_ok=exist_ok)
    File "/opt/ilastik-1.4.0-Linux/lib/python3.7/os.py", line 223, in makedirs
      mkdir(name, mode)
  PermissionError: [Errno 13] Permission denied: '/.cache'

I've left it in the code, but commented it out for now.

I tried setting MPLCONFIGDIR in illastik/pixelclassification/main.nf just before the call to run_ilastik.sh, but that didn't help. I still get the same error.
Oh, I think I see. That might fix the issue with matplotlib, but the problem is that something else is trying to write to .config and it doesn't have permission. I'm not sure how to fix this.

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RobJY avatar RobJY commented on August 17, 2024

Workflow now running with the modules: ashlar, deepcell_mesmer & mcquant. It also performs input validation on the sample and marker sheets.

Needs clean-up and nf-tests, but added end-to-end test using pytest.

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RobJY avatar RobJY commented on August 17, 2024

Current commands to run workflow and tests:

nextflow run ~/github/mcmicro-nf-core/main.nf --input_cycle ~/github/mcmicro-nf-core/assets/samplesheet_1_row_sample_cycle.csv --outdir ./output --marker_sheet ~/github/mcmicro-nf-core/assets/markers_1.csv -profile test_work -params-file ~/github/mcmicro-nf-core/conf/workflow.json

From base repo dir:
nf-test test tests/main.nf.test --profile test_work
nf-core lint

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