Ncov git pull update

Hi,

what is the best way to update locally GitHub - nextstrain/ncov: Nextstrain build for novel coronavirus SARS-CoV-2 after a git clone on my server ?
I have tried git pull --ff-only origin master as suggested in the tutorial but I always have to git reset some files because of the following error;
error: Your local changes to the following files would be overwritten by merge:
** defaults/color_ordering.tsv**
** defaults/exclude.txt**
** scripts/developer_scripts/parse_additional_info.py**
** and many other**
Please commit your changes or stash them before you merge

Thanks,
Eric

Hi @Eric. Hmm. It’s not clear exactly why git thinks a lot of files have been modified in your local copy. Can you run these commands and attach the output file here? It will tell us why git thinks the files have changed.

# Stage all files, just temporarily; doesn't change them
git add .

# Get detailed status report
git status --porcelain=v2 > status.txt

# Unstage all files, leaving you back where you started
git reset

Our suspicion is that file modes are the problem here, but it’s hard to know for sure without the status report.

Hi Thomas,

I think my ncov version was simply corrupted. I just cloned a new one and it didn’t appens anymore.

Thank you
Eric