spring-clean: DeepARG

Dependency: DeepARG

git submodule
rm dir. in scripts/
rm git clone from set-up.sh
update path in config.yaml
set-up commands: replace path and make DIAMOND bin executable

git lfs install # if not already done
git submodule add https://gaarangoa@bitbucket.org/gusphdproj/deeparg-ss.git submodules/deeparg-ss
cd submodules/deeparg-ss/
git checkout 14b8dce

Impact: Could affect the results if there are any discrepancies between the versions of any dependency. Therefore:

Confirm git version
Use same YAML as in original repo

Edited Apr 21, 2020 by Valentina Galata