@robertH: Some of your command line “dashes” are actually unicode U+2013 chars. Try replacing them with ASCII “dashes” U+002D. (Otherwise this might just be a transcription issue related to your posting.)
This workaround goes into the right direction. After calling the program through the proposed java command line, the jar file could be found and Amiris seems to start correctly.
However, an important step in this workaround seems to be missing because no input.pb and log4.properties files are generated. Therefore, the calculation is aborted.
In constrast, if I am running first
!amiris run -j /content/amiris-core_22.214.171.124-jar-with-dependencies.jar …
the input.pb file is generated (even if the calculation is aborted at a late stage). With this input.pb file in the working directory it is possible to run amiris and generate the output folder. Nevertheless, this do not lead to proper results (not surprising, because of missing data in log4j.properties).
Which command lines should be added to generate the missing files (input.pb, log4j.proberties)? Unfortunately I could not find sufficient information in the amiris wiki.
I have noticed a minor inconsistency in my previous post.
Therefore, I have updated the instructions by naming the file to create input.pb (default: config.pb):
!makeFameRunConfig -f scenario.yaml -o input.pb
The log4j.properties file is downloaded (together with fameSetup.yaml, and the amiris.jar files) when executing amirispys’ amiris install. This command is executed only once in order to setup your amiris installation properly.