Hi there! (I’ll page @petebankhead already because I imagine he’ll be the one to answer this one.)
We’re in the process of offering all image analysis tools as Singularity containers so that they can be run directly in our clusters with access to fast storage - it’s been a mostly successful enterprise but we’ve run into problems with QuPath! I’m generating a super simple singularity container with the following recipe:
Bootstrap: docker From: ubuntu:xenial %runscript cd /qupath/QuPath ./QuPath %post mkdir /qupath cd /qupath apt-get update apt-get install -y wget wget https://github.com/qupath/qupath/releases/download/v0.1.2/QuPath-0.1.2.tar.gz tar xvvf QuPath-0.1.2.tar.gz rm QuPath-0.1.2.tar.gz
As you can see I’m going back to 0.1.2 just in case, and using Ubuntu 16.04 as suggested here. When I try to run this container, the only output I get is:
./qupath.sif 15:24:47.704 [main] [INFO ] qupath.QuPath - Launching QuPath with args: QuPath Error invoking method. QuPath Failed to launch JVM
Am I missing something? Do I need to install JRE/JDK separately? I looked around in the container for log files but couldn’t find on the QuPath folder. Any help appreciated!