I use my conda installed Galaxy instance and ran into a problem using the tool “Merge BAM Files” v1.2.0
It outpus the error:
Error: Unable to access jarfile /MergeSamFiles.jar
From the command line I can see that it sets $JAVA_JAR_PATH in front, but as this env variable is empty, the jar file is not found. I found it though in my galaxy/database/dependencies/_conda/pkgs/picard-1.56-1/share/picard-1.56-1 directory. Even if I manually set the JAVA_JAR_PATH env in the environment where I start galaxy, it won’t work. Where is the correct envirnment to look for, to set the variable or did I miss anything else?
I already tried reinstalling the tool and also Picard.