generate_report_from_template writes to path where package is installed

[agitter]

If I'm reading the source code correctly, generate_report_from_template calls format_script and writes to a file path relative to where DOMINO is installed:

DOMINO/src/utils/visualize_modules.py

Line 169 in 85dad15

report_file_name=format_script(os.path.join(os.path.dirname(os.path.abspath(__file__)),'../data', "graph.html"), NUM_OF_GENES=len([x for x in cy if not "source" in x["data"] and len(x["data"]["modules"])>0]), HG_REPORT=[], MODULES_SUMMARY=[], DISEASE_GENES=[], DATA=json.dumps(cy))

I'm attempting to run DOMINO inside a Singularity container where I don't have write permission to create files at that location. The package was installed by root when the image was created, and now I am running as my user.

Making the file paths configurable or using Python's temporary directories would avoid this problem.