The term 'bioformats2raw' is not recognized as a name of a cmdlet

[AmmarAmmer]

I installed python-blosc from (http://python-blosc.blosc.org/install.html). All tests were sucessful:

Doctest: blosc.toplevel.unpack_array ... ok Ran 39 tests in 4.976s OK

I put blosc.dll in the same folder

After that, I set up the path with:

set JAVA_OPTS="-Djna.library.path=C:\python-blosc"

and put blosc.dll in the same folder

At the last I installed the libraries with:

conda install -c ome bioformats2raw raw2ometiff

When I use: bioformats2raw /path/to/file.mrxs /path/to/zarr-pyramid

I get the message (The term 'bioformats2raw' is not recognized as a name of a cmdlet)

What I'm doing wrong? Thanks

[melissalinkert]

Errors like that usually mean that the PATH environment variable doesn't include the folder where bioformats2raw.bat and raw2ometiff.bat are installed. If you are not running bioformats2raw from an Anaconda Prompt, either add the correct folder to the PATH environment variable, or specify the full path to bioformats2raw.bat instead of just bioformats2raw. You might also try running bioformats2raw from an Anaconda Prompt instead of PowerShell.

If that doesn't help, https://github.com/ome/conda-bioformats2raw is the better place to ask questions about the Conda package. The OME team maintains that package separately from bioformats2raw itself.

Closing here since I can't transfer the issue to https://github.com/ome/conda-bioformats2raw.