CellProfiler Nightly Permission denied error=13

[wmyu]

I am trying to run the sample workflow CellProfiler_Human on a MAC and ran into the following error:

ERROR CellProfiler Pipeline Executor 2:4        Execute failed: Cannot run program "/Applications/CellProfiler-nightly.app/": error=13, Permission denied

Every setp of the instruction how to execute the workflow was followed.   There was a previous thread (~2 years ago about the same issue) but offered no final solution.  Does anyone knows how to use CellProfiler with KNIME in a MAC OS?  Any help will be highly appreciated.

 

[christian.birkhold]

Hi wmyu,

Maybe you have to run KNIME with admin rights in order to execute CellProfiler from within KNIME?

Best,

Christian

[Keisuke]

hi,

I’m having the same issue with KNIME (3.7.0) calling Cell Profiler in MacOS

ERROR CellProfiler Pipeline Executor 2:4 Execute failed: Cannot run program “/Applications/CellProfiler-3.1.8.app/”: error=13, Permission denied

The result is the same when launching KNIME with admin rights using the sudo command.

Does anyone have a solution to this? Anyone using Cell Profiler integration in MacOS?

Keisuke

[stelfrich]

Hi @Keisuke,

Could you please follow the instructions to add the KNIME Image Processing nightly updatesite. Once you have done that you should be able install a more recent version of the CellProfiler integration with a bugfix for what you are experiencing (at least the same error message has motivated my bugfix).

Let me know if you need additional pointers and/or if it works!

Best,
Stefan

[Keisuke]

Thanks, Stefan! This solved the issue, and I could run this example workflow.

Keisuke