Relative path issue when running not in the repo directory

[gongyixiao]

When running without docker ENTRYPOINT mode, when below command is used:

cd [some_dir]
python [path_to_neoantigen-vaccine-pipeline]/run_snakemake.py

The current working directory is some_dir

And this line:

neoantigen-vaccine-pipeline/run_snakemake.py

Line 274 in d2af22c

'pipeline/Snakefile',

It will interpret the relative path from some_dir and think pipeline/reference_Snakefile is in
[some_dir]/pipeline/reference_Snakefile, but in fact it is in [path_to_neoantigen-vaccine-pipeline]/pipeline/reference_Snakefile

It's not appropriate to assume people will run run_snakemake.py from the [path_to_neoantigen-vaccine-pipeline] all the time.

This is critical when running in singularity because you need to be able to run python [path_to_neoantigen-vaccine-pipeline] outside of the singularity container to for example submit a singularity job.

I purpose the following change which won't change any current behavior but at the same time fix the issue:

neoantigen-vaccine-pipeline/run_snakemake.py

Line 21 in d2af22c

from os.path import dirname, isfile, join, basename, splitext, exists

Change to:

from os.path import dirname, isfile, join, basename, splitext, exists, realpath

neoantigen-vaccine-pipeline/run_snakemake.py

Line 274 in d2af22c

'pipeline/Snakefile',

Change to:

dirname(realpath(__file__))+'/'+'pipeline/reference_Snakefile',

neoantigen-vaccine-pipeline/run_snakemake.py

Line 305 in d2af22c

'pipeline/reference_Snakefile',

Change to:

dirname(realpath(__file__))+'/'+'pipeline/reference_Snakefile',