Closed dunleavy005 closed 6 years ago
If you run with PARTIS=/your/partis/install/path ./process_partis.py ...
, it should work.
That having been said, it should/could be data/...
instead of /data/...
.
So I originally ran this using your error message, like:
export PARTIS=$PWD/partis
bin/process_partis.py .....
and this definitely did not work. I did some experimenting with os.path.join
and I found anytime I took off the front-slash from the 2nd path to be joined, the two paths would merge, otherwise not. I realized I probably won't need to use default germline files so its a moot point, but it seems as it is default germline file paths aren't properly joining (unless I'm missing something in my setup).
So it is! Good catch.
Hi,
In
process_partis.py
, line 41default_germline_sets = os.path.join(partis_path, '/data/germlines/human')
isn't doing what it's supposed to be doing. It always outputs/data/germlines/human
, I did some tinkering and found that the line should bedefault_germline_sets = os.path.join(partis_path, 'data/germlines/human')
with no front-facing blackslash. Can someone confirm this please (or at least be willing to make the change on master branch)?