README example does not work for running fpocket in a docker container

[czabriskie]

Describe the bug README example does not work for running fpocket in a docker container. The WORKDIR is incorrect and when changed to the correct WORKDIR, fpocket still doesn't produce the output expected.

To Reproduce Steps to reproduce the behavior:

1. Pull or build docker image as described docker pull fpocket/fpocket or docker build -t fpocket/fpocket .
2. run command as described on example dataset docker run -vpwd:/WORKDIR fpocket/fpocket fpocket -f data/sample/1UYD.pdb
3. Look for output

System Properties Operating System

Distributor ID: Ubuntu
Description:    Ubuntu 20.04.6 LTS
Release:    20.04
Codename:   focal

Docker Version

24.0.7, build afdd53b

Platform

amd/64

Expected behavior Data should be mounted and accessible to the container. fpocket should run on the file and output received

Output when running example

! File data/sample/1uyd.pdb does not exist
! File data/sample/1uyd.pdb does not exist
! Structure reading failed!
***** POCKET HUNTING BEGINS ***** 

Output when modifying mount location to /tmp (The WORKDIR specified in the Dockerfile-debian-slim file)

***** POCKET HUNTING BEGINS ***** 

with no ***** POCKET HUNTING ENDS ***** as described and no output folder/file created as expected

[czabriskie]

Running it locally works fine, but something odd happens when running it in a container. I can even edit the image so I can move into the container and run fpocket fine, but it doesn't like the mount for some reason.

[pschmidtke]

thanks for reporting this. There was a change recently in how to run it in /tmp folders as this was requested by another user, it might have impacted this one. Let me see if I can add this as automated test as well.

[pschmidtke]

Updated in documentation for Release 4.2