Running ROADIES Singularity Image (roadies.sif) - Missing Scripts/Dependencies #45
Description
I'm encountering problems when running the ROADIES Singularity image (roadies.sif). The container cannot find the run_roadies.py script or other dependency files. The initial error message was:
usr/local/bin/python: can't open file '/data1/user/liuyunj/test/image/ROADIES/run_roadies.py': [Errno 2] No such file or directory
After investigating with singularity exec roadies.sif find / -name "run_roadies.py" 2>/dev/null, I found the correct path and was able to execute:
singularity exec roadies.sif python /usr/local/ROADIES/run_roadies.py --help
This command worked normally.
However, when I tried to run the full command:
singularity exec roadies.sif python /usr/local/ROADIES/run_roadies.py --cores 10
I encountered the following error:
python: can't open file '/data1/user/liuyunj/test/image/ROADIES/workflow/scripts/noconverge.py': [Errno 2] No such file or directory
Traceback (most recent call last):
File "/usr/local/ROADIES/run_roadies.py", line 17, in
subprocess.run(
File "/usr/local/lib/python3.9/subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['python', 'workflow/scripts/noconverge.py', '--cores', '10', '--mode', 'accurate', '--config', 'config.yaml']' returned non-zero exit status 2.
I downloaded the image using:
singularity pull roadies.sif https://depot.galaxyproject.org/singularity/roadies:0.1.4--py39h4577df3_0
Could you please advise on how to properly use this image? Would it be possible to provide detailed instructions on the correct usage?