search

flass / pantagruel

a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
GNU General Public License v3.0
46 stars 7 forks source link

links in generated outputs #2

Closed pveber closed 5 years ago

pveber commented 5 years ago

In step 0 (among others), we create symbolic links to input data. It would help to create relative links instead of absolute. This is necessary for bistro integration and better in general (an analysis directory can then be moved around without breaking links). This can be done with realpath, see this example.

flass commented 5 years ago

very good point! this has been fixed thoughout the pipeline in commit 0167cdd using code like ln -s $(realpath --relative-to=$(dirname dest) src) dest Cheers! Florent