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refgenie / refgenconf

A Python object for standardized reference genome assets.
http://refgenie.databio.org
BSD 2-Clause "Simplified" License
3 stars 6 forks source link

alias links to log files appear to be wrong #122

Closed nsheff closed 3 years ago

nsheff commented 3 years ago

The refgenie alias dir uses symlinks to point to the data dir. These links are correct on our main rivanna genomes directory: image

But when I build for a new server, I see this:

image

The links point to the wrong level, I think they need 5 ../ levels rather than 4.

nsheff commented 3 years ago

maybe this issue should be in refgenconf in the _symlink_alias function

stolarczyk commented 3 years ago

did you try running some test builds again? The assets I built for rg.databio.org a couple of days ago have functional symlinks: $PROJECT/deploy/rg.databio.org/genomes/alias/hg38/fasta/default. Is it possible that this is somehow specific to your setup?

stolarczyk commented 3 years ago

ah ok, I see the issue. It's about files in _refgenie_build only

stolarczyk commented 3 years ago

e.g. here: $PROJECT/deploy/rg.databio.org/genomes/alias/hg38/fasta/default/_refgenie_build