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kmansouri / OPERA

Free and open-source application (command line and GUI) providing QSAR models predictions as well as applicability domain and accuracy assessment for physicochemical properties, environmental fate and toxicological endpoints. ==================>Download the latest compiled version from the "releases" tab and run the executable installer.
MIT License
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Knime workflow is missing in OPERA2.9_CL_par #36

Closed tsufz closed 1 year ago

tsufz commented 1 year ago 
LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/v912/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v912/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v912/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v912/sys/opengl/lib/glnxa64

 All properties will be calculated: 
General structural properties, Physchem, Env. fate, ADME and Tox Endpoints (CERAPP, CoMPARA and CATMoS)  

 Initializing and loading models...

========== Structures standardization ==========
Input structures: 3353.
Generating QSAR-ready structures...
Error using OPERA_par
No matching files named '/usr/OPERA/application/knime_4.5.1/knime-workspace/QSAR-ready_2.5.10' were found.

System: Ubuntu 22-04

Yours Tobias

tsufz commented 1 year ago

Okay, as workaround, I installed 1) the mcr installation and then 2) the par application. However, in addition, the workflow is expected in the home folder not inside of the OPERA directory. 


Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/v912/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v912/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v912/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v912/sys/opengl/lib/glnxa64

 All properties will be calculated: 
General structural properties, Physchem, Env. fate, ADME and Tox Endpoints (CERAPP, CoMPARA and CATMoS)  

 Initializing and loading models...

========== Structures standardization ==========
Input structures: 3353.
Generating QSAR-ready structures...
CompileCommand: exclude javax/swing/text/GlyphView.getBreakSpot
Apr 20, 2023 9:11:55 AM org.apache.cxf.bus.osgi.CXFExtensionBundleListener addExtensions
INFO: Adding the extensions from bundle org.apache.cxf.cxf-rt-frontend-jaxrs (402) [org.apache.cxf.jaxrs.JAXRSBindingFactory]
Apr 20, 2023 9:11:55 AM org.apache.cxf.bus.osgi.CXFExtensionBundleListener addExtensions
INFO: Adding the extensions from bundle org.apache.cxf.cxf-rt-transports-http (405) [org.apache.cxf.transport.http.HTTPTransportFactory, org.apache.cxf.transport.http.HTTPWSDLExtensionLoader, org.apache.cxf.transport.http.policy.HTTPClientAssertionBuilder, org.apache.cxf.transport.http.policy.HTTPServerAssertionBuilder, org.apache.cxf.transport.http.policy.NoOpPolicyInterceptorProvider]
Apr 20, 2023 9:11:55 AM org.apache.cxf.bus.osgi.CXFExtensionBundleListener addExtensions
INFO: Adding the extensions from bundle org.apache.cxf.cxf-rt-transports-http-hc (406) [org.apache.cxf.transport.http.HTTPConduitFactory, org.apache.cxf.transport.ConduitInitiator]
ERROR    main BatchExecutor  IO error while loading the workflow: No workflow directory at /home/xxx/knime-workspace/QSAR-ready_2.5.10
Apr 20, 2023 9:11:55 AM org.apache.cxf.bus.osgi.CXFExtensionBundleListener unregister
INFO: Removing the extensions for bundle 402
Apr 20, 2023 9:11:55 AM org.apache.cxf.bus.osgi.CXFExtensionBundleListener unregister
INFO: Removing the extensions for bundle 405
Apr 20, 2023 9:11:55 AM org.apache.cxf.bus.osgi.CXFExtensionBundleListener unregister
INFO: Removing the extensions for bundle 406

Error using OPERA_par
Standardization process failed. Check the input file.

``
kmansouri commented 1 year ago

Hi Tobias, Yes, the parallel version did not include the workflow because of the github package size limitation. I am working on a solution for that. In the meanwhile, you can run the regular command line version or the GUI once and it'll initialize the workflow. Then you can use the parallel version. Thanks

tsufz commented 1 year ago

@kmansouri, thanks for your detailed answer. I already found that solution.