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knime-ip / knip-cellprofiler

KNIME Image Processing - CellProfiler Integration
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Set CellProfiler Path on Directory, not on file #5

Closed dietzc closed 9 years ago

dietzc commented 9 years ago

Currently, the user has to set the path to a dedicated file in the CellProfiler directory in the KNIME Image Processing Properties. We want to change that, that the user only has to point on his local installation of CellProfiler!

LeeKamentsky commented 9 years ago

I'm guessing you have defaults for the paths that are usually correct. The default for Windows is "C:\Program Files\CellProfiler" and, if you want to use a roundabout way to find it, you can look in the Windows registry for "HKEY_CLASSES_ROOT\CellProfilerProject\shell\open\command".

CellProfiler installs to /Applications/CellProfiler.app on the Mac and the analysis worker is at /Applications/CellProfiler.app/Resources/MacOS/CellProfiler.

If you install on Centos using the RPMs, "/usr/bin/cellprofiler" will start CellProfiler, so you should be able to find it on the $PATH.

I had set things up so that if you used the analysis_worker command-line switch, "--work-announce", when starting CellProfiler, it would redirect to analysis_worker. https://github.com/CellProfiler/CellProfiler/commit/907c804523ddfdfa2609f0059d06306822a203de adds "--knime-bridge-address" to the list of switches that will start the analysis_worker instead of CellProfiler, so after today, Knime should be able to run the CellProfiler binary like this:

cellprofiler --knime-bridge-address=tcp:127.0.0.1:xxxx

and not have to rely on the analysis_worker script if there is a binary installation.

dietzc commented 9 years ago

great! thank you! I will use these changes

dietzc commented 9 years ago

done in https://github.com/knime-ip/knip-cellprofiler/commit/45f1b3b1a5f0c4b421c8b7d33947cecd739d79d7