I have pulled a Docker container to create the .sif file
apptainer pull docker://mblanche/ngmerge:latest
there is no documentation so I have explored the sif file to know where is the tool I want to use is.
apptainer run /mainfs/wrgl/broadinstitute_warp_development/warp/images/manuel_images/ngmerge_latest.sif /bin/bash
# In the container I have found the tool
cd /
cd NGmerge/
ls
LICENSE Makefile NEWS NGmerge.c NGmerge.h README.md UserGuide.pdf VERSION figures qual_profile.txt scripts
# If I do
NGmerge
# The tool is run
The executable NGmerge works when I'm in its directory because (I think) the current directory (.) is in the PATH. However, when trying to execute it directly with the full path from outside the container or in the container from another directory, it's not being found, indicating a potential issue with the path or executable.
How can I run the executable in this situation??