Hi, thank you so much for the tool. Our compute cluster doesn’t support docker so we converted the docker image to a singularity image. As per the instructions, we installed the separate software (MSPminer, Interproscan, etc.) outside the container and made sure all the relevant paths were in our $PATH. However, none of these softwares could be recognized within the container, e.g. this command didn’t recognize that MSPminer, Interoproscan, etc. were successfully installed:
singularity run -B <path_to_where_tools_are_stored> --env PATH=$PATH <path_to_metaWIBELE_sandbox> metawibele_check_install
First, did you check the executable files of MSPminer and Interproscan are on your host $PATH? If they are all set on the host environment, then you might try executing the tools in the container directly to see if there are any error messages for the tools, e.g. “$ mspminer”, “$ interproscan.sh -version”, which might determine if 1) they can’t be found or 2) they are not executable or 3) a different install error that we can then debug further.
I am working with meenachakra on this installation. Thank you so much for your quick reply. I tested $ mspminer and $ interproscan.sh -version outside of the container and it can find them without issue. Inside the container, I get errors like the following:
FATAL: "interproscan.sh": executable file not found in $PATH
So it seems like it is scenario 1) in that they can’t be found. Let me know what I can try next. Thank you!!
It looks like your host environment $PTAH including MSPminer and Interproscan might not be well passed to the singularity container. You may need to figure it out how to pass the host $PATH variable to the container, e.g. some discussion about this: https://groups.google.com/a/lbl.gov/g/singularity/c/4uacpEamUCc Hope it helps!