This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Unable to access jar file in Docker image

I am loading a Docker image and trying to run under Shifter. However, I had the following error: "Unable to access jarfile pilon-1.23.jar"

My script is here: shifter --image=ttubb/pilon java -Xmx60G -jar pilon-1.23.jar

Here is the link to the docker image: https://hub.docker.com/r/ttubb/pilon/dockerfile

I guess that the jar file would be saved under a specific folder name, however, I cannot locate the folder. If you know any tips of finding the jar file location, could you please tell me how to do it? It will be of great help and learning for me.

Thanks.

genome

1 answer

Hello, as docker file WORKDIR /software, so .jar will under /software, maybe /software/pilon.jar.

I don't know Shifter, but on linux, you can run docker image use interactive mode(-it), which way you can search your files derictly "inside" container. Maybe you can google how to run docker interactive mode on Shifter.

Thank you very much. I found the jar file under /software. I will also check how to run docker interactive mode on Shifter for my future use.

Many thanks.

Log in to answer this question.