version 4.0.0 docker issue

[bltsai-UCLA]

I would just like to point out that the 4.0.0 release may have a docker issue:
docker run -it --rm prvst/philosopher:4.0.0 /bin/bash
docker: Error response from daemon: unable to find user biodocker: no matching entries in passwd file.

2 solutions that resolve this issue are:
docker run -it --rm --user daemon prvst/philosopher:4.0.0 /bin/bash
docker run -it --rm --user $(id -u) prvst/philosopher:4.0.0 /bin/bash

It's also noticable that version does not have this issue:
docker run -it --rm prvst/philosopher:3.4.13 /bin/bash

[bltsai-UCLA]

Another issue in version 4.0.0 that was working in 3.4.13:
java -jar MSFragger --config
java: command not found

[prvst]

Hi @bltsai-UCLA. I pushed a new image to Docker Hub, you can try running again. Also, the container only contains Philosopher, if you want to un MSFragger as well, you will have to add it yourself.

[bltsai-UCLA]

Thanks! The new image resolved the --user issue. However, it still seems like the container does not contain java, "java: command not found"

[prvst]

That is correct. We had to move away from the biocontainers base image, which had different software pre-installed, including Java. The new base image is a plain Ubuntu one, so you will have to install Java on it.