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BD2KGenomics / toil-lib

A common library for functions and tools used in toil-based pipelines
Apache License 2.0
4 stars 7 forks source link

FileIOStore symlinks don't work with docker #82

Closed glennhickey closed 7 years ago

glennhickey commented 7 years ago

The current implementation creates symlinks in read_input_file that don't work with docker. Changing this to copy, ex https://github.com/glennhickey/toil-lib/commit/61840bc1ad2c7e3dc6c698eccf835533bf30cca9 is required for toil-vg, or at least was a few months ago.

glennhickey commented 7 years ago

Looks like I'm confused between this toil-lib and Charlie's toil-lib, which aren't related as I thought.