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roblanf / sarscov2phylo

Global phylogenies of SARS-CoV-2 sequences
GNU General Public License v3.0
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tree_ft.sh file does not exist #19

Closed youngDouble closed 3 years ago

youngDouble commented 3 years ago

Version: release 13-11-20 I noticed that thetree_ft.sh file does not exist in the scripts folder scripts/global_tree_gisaid.sh: bash $DIR/tree_ft.sh -i $outputfasta -t $threads Where can I get tree_ft.sh ?

AngieHinrichs commented 3 years ago

tree_ft.sh was removed in 55cbb8ddaddaceb2ecd0577f105a3fd37f13d304. You can make a fork of this repo in Github, clone your fork on the command line and bring back the script with 'git revert 55cbb8dd'.

roblanf commented 3 years ago

Thanks @AngieHinrichs.

@youngDouble: to add a bit more detail, the repo contains a few old scripts that I no longer use. In particular, I used to build the tree from scratch at every update, but I moved to iteratively improving the tree instead because this is a better approach (in terms of speed and accuracy) for this situation where we get a small amount of new data every day. tree_ft.sh is one of those older scripts that I did remove.

However, you're not the first person that has wanted to use that, so I'll give a bit of thought to how best to clean up the repo so it includes clear information on both:

  1. De-novo phylogenetics for SARS-CoV-2 (i.e. starting from scratch each time)
  2. Online phylogenetics (which is what the readme runs through).

Thoughts welcome.

Rob